This is actually a sub-topic of the strength & conditioning books. This is because program design and periodization, though form a part of strength & conditioning gamut, are an extensive topic among itself.

Here are my top recommendations:

1.Periodization Training for Sports – Tudor Bompa –  Dr. Tudor Bompa pioneered most of these breakthroughs, proving long ago that it’s not only how much and how hard an athlete works but also when and what work is done that determine an athlete’s conditioning level. Periodization Training for Sports goes beyond the simple application of bodybuilding or powerlifting programs to build strength in athletes. 

In this new edition of Periodization Training for Sports, Bompa teams with strength and conditioning expert Carlo Buzzichelli to demonstrate how to use periodized workouts to peak at optimal times by manipulating strength training variables through six training phases (anatomical adaptation, hypertrophy, maximum strength, conversion to specific strength, maintenance, and tapering) and integrating them with energy system training and nutrition strategies. Coaches and athletes in 35 sports have at their fingertips a proven program that is sure to produce the best results. No more guessing about preseason conditioning, in-season workloads, or rest and recovery periods; now it’s simply a matter of identifying and implementing the information in this book. 

Presented with plenty of ready-made training schedules, Periodization Training for Sports is your best conditioning planner if you want to know what works, why it works, and when it works in the training room and on the practice field.

2.Periodization – Tudor Bompa-this book offers information central to understanding the latest research and practices related to training theory while providing scientific support for the fundamental principles of periodization.

This definitive text presents a comprehensive discussion of periodization based on the philosophy of Tudor Bompa. It features the following:

• A review of the history, terms, and theories related to periodization

• Discussion of the importance of designing a sport-specific and
  competition-level annual plan and discarding any one-size-fits-all approach

• An expanded chapter on the integration of biomotor abilities within the training process

• Comprehensive updates to the information on training sessions,
  microcycles, and macrocycles

• An expanded chapter on the methods for developing muscle strength,including manipulation of loading variables and the conversion to specific strength

• A more detailed explanation of speed and agility training, differentiating between individual and team sports

In addition to applying periodization models to resistance training, Periodization also discusses sport-specific endurance. You’ll be introduced to different methods of testing and developing endurance, including the physiological basis for each method.

3.Practical Programming for Strength Training – Mark Rippetoe-there is a difference between Exercise and Training. Exercise is physical activity for its own sake, a workout done for the effect it produces today, during the workout or right after you’re through. Training is physical activity done with a longer-term goal in mind, the constituent workouts of which are specifically designed to produce that goal. Training is how athletes prepare to win, and how all motivated people approach physical preparation.

Practical Programming for Strength Training, addresses the topic of Training. It details the mechanics of the process, from the basic physiology of adaptation to the specific programs that apply these principles to novice, intermediate, and advanced lifters.

• Better explanations of the proven programs that have been helping hundreds of thousands of lifters get stronger more efficiently
• Details of 3 different approaches to the problem of getting stuck and special approaches for the underweight and overweight trainee

• Intermediate chapter with 18 separate programs and 11 detailed
  examples

• Advanced chapter with detailed examples of 9 different programs

• Special Populations chapter with example programs for women and
  masters lifters training through their 50s, 60s, 70s, and 80s

• Day-to-day, workout-to-workout, week-by-week detailed programs for every level of training advancement
• The most comprehensive book on the theory and practice of programming for strength training in print

4.Designing Resistance Training Programs – Steven J. Fleck & William J.Kraemer-it is a guide to developing individualized training programs for both serious athletes and fitness enthusiasts. In this book, two of the world’s leading experts on strength training explore how to design scientifically based resistance training programs, modify and adapt programs to meet the needs of special populations, and apply the elements of program design in the real world.

Fleck and Kraemer provide readers with a thorough understanding of the process of designing resistance training programs from both scientific and practical perspectives. Designing Resistance Training Programs, is the only resource available that presents the body of research in the field in this organized and comprehensive format.

Designing Resistance Training Programs, begins by outlining the
principles of resistance training and exercise prescription, and examines the various types of strength training,including isometrics and eccentric training. This is followed by a adiscussion of resistance training from a physiological perspective and an overview of how resistance training programs interact with the other conditioning components such as aerobic, interval, plyometric, and flexibility training. Readers will then explore advanced training techniques, how to manipulate training variables in a long-term resistance training program, and ways to plan rest into long-term training that minimizes losses in fitness or performance gains

An important text for students, researchers, and practitioners, this textbook offers the information and tools to help readers evaluate resistance training programs and better understand the context and efficacy of new data findings in this ever-changing field. Designing Resistance Training Programs, is an essential resource for understanding the science behind resistance training and designing evidence-based resistance training programs for any population. This text provides the
tools for understanding and designing resistance training programs for almost any situation or need.

5.NSCA’s Guide to Program Design – Jay R. Hoffman-this book offers the most current information, guidance, and protocols from respected scientists and practitioners with expertise in strength and conditioning program design. Developed by the National Strength and Conditioning Association (NSCA),this text offers strength and conditioning professionals a scientific basis for developing training programs for specific athletes at specific times of year. Straightforward and accessible, NSCA’s Guide to Program Design presents a detailed examination of considerations and challenges in developing a program for each key fitness component and fitness performance goal.

This authoritative text moves beyond the simple template presentation of program design to help readers grasp the reasons and procedures for sequencing training in a safe, sport-specific manner. The text offers 20 tables that are sample workouts or training plans for athletes in a variety of sports, technique photos and instructions for select drills, and a sample annual training plan that shows how to assemble all the pieces previously presented. Plus, extensive references offer starting points for continued study and professional enrichment.

NSCA’s Guide to Program Design progresses sequentially through the program design process. It begins by examining the athlete needs assessment process as well as performance testing considerations and selection. Next, performance-related information on both dynamic warm-up and static stretching is discussed and dynamic warm-up protocols and exercises are presented. Then it reveals an in-depth by-chapter look at program design for resistance, power, anaerobic, endurance, agility, speed, and balance and stability training. For each, considerations and adaptations are examined, strategies and methods are discussed, and evidence-based information on program development is presented.

The final two chapters help you put it all together with a discussion of training integration, periodization, and implementation. NSCA’s Guide to Program Design helps bridge the gap between scientist and practitioner by providing coaches and other strength and conditioning professionals with evidence-based information and applications.

6. The System: Soviet Periodization Adapted for the American Strength Coach – Johny Parker, Al Miller & Rob Panariello-despite a seemingly endless supply of training programs promising enhanced athletic performance, the same questions inevitably plague strength and conditioning coaches. How do you initiate an athlete’s strength program and progress it over the course of not just a season, but a career? How will you know when it is time to progress, and how can you avoid the consequences of overtraining? How can you develop an athlete’s work capacity while increasing strength, power, and speed without completely sacrificing one quality for another?

The answer to all of those questions lies in the systematic approach to program design outlined in The System.

Hall of Fame strength coaches Johnny Parker, Al Miller, and Rob Panariello have spent their entire careers studying, testing, and refining the best practices and methods of Soviet-era sports science into a modern, practical approach to strength and conditioning for long-term athletic development. Their system of scientific programming and coaching produced not only powerful and resilient athletes, but also dominant championship teams spanning over three decades.

Their distilled lessons and experiences will teach you:

• A structured approach to advance a novice athlete to a stronger and more powerful performer
• Why simplicity in exercise selection is one key to athletic development
• The critical training variables that can make or break progress
• How planned—not random—variations in training will yield progressive and sustained physical gains
• How to integrate lifting, running, and jumping together to build explosive athletes

This book provides more than just a system of principles for optimal strength and conditioning program design. Rather, it provides an education in both the science and the art of coaching and will help you develop what the authors call the “Eye of the Coach” to ensure continued success for both you and your athletes.

7.Strength Training Manual: The Agile Periodization Approach
(Volume One & Two: Theory Book 1) – Mladen Jovanovic-this text represents my ongoing pursuit in understanding both strength training and training theory in general, by providing an overview of the conflicting opinions, but also giving practical, heuristic solutions to common problems and their reconciliation. The framework for such an approach is the Agile Periodization, which approaches planning from uncertainty perspective, iterations, and experimentation while providing satisficing and robust solutions.

Besides being very rich in theory, Strength Training Manual is also rich in forum-for-action solutions, including reference tables, useful heuristics,and more than 1,900 set and rep schemes provided and analyzed. It also provides the best practices from other experts tinkering in this field.
This text covers the following topics:

• The philosophical underpinning of the Agile Periodization
• Exercise classifications and their relationships
• Testing approaches for establishing 1RM used for percent-based prescription as well as the novel Estimation through iteration approach
• Prescribing training loads using various methods and their modifications
• A thorough discussion of the training dose concept, as well as dose ->
  response models
• Anatomy of set and rep schemes and their archetypal variants
• Mladen’s Methodological System of classifying Set and Rep schemes
• Horizontal and Vertical planning perspectives (This will cut through all the periodization crap you have been fed over the years)
• Novel planning strategies and concepts such as robustness, microdosing, Don’t break the chainand Markov Chain
• A thorough discussion on what individualization really is (and what it should be)
• Review and Retrospective practices including updating planning 1RMs between phases and phase potentiation ideas and critiques (and novel iterative approach)
• Discussion on predictive and causal modeling in strength training

Strength Training Manual will give you not only a practical solution to tackle everyday problems of planning, prescribing, and monitoring strength training, but also critical thinking skills. You can use these essential skills of thinking and tools in other types of physical preparation and training in general.

8.Advanced Fitness Assessment & Exercise Prescription – Ann Gibson, Dale Wagner & Vivian Heyward-this text provides a comprehensive approach to physical fitness appraisal and customized exercise prescription. The text synthesizes research and practice with concepts and theories from exercise physiology, kinesiology, measurement, psychology, and nutrition to clearly convey how assessments from physical fitness testing inform the design of individualized exercise programs.

Advanced Fitness Assessment and Exercise Prescription reflects the latest exercise testing and prescription guidelines from the American College of Sports Medicine (ACSM) as well as physical activity recommendations from the U.S. government and American Heart Association. It also takes into account recent ACSM guidelines for medical exam and exercise testing requirements to consider before beginning exercise programs.

The assessment and testing protocols in Advanced Fitness Assessment and Exercise Prescription, is structured around five physical fitness components: cardiorespiratory endurance, muscular fitness (strength,endurance, and power), body composition, flexibility, and balance. The text begins with an overview of physical activity, health, and chronic disease, including a discussion of preliminary health screening and risk classification. It then leads into field and laboratory assessment and testing protocols, followed by prescription guidelines for designing exercise programs to improve each fitness component. Readers will find the latest information on maximal and submaximal graded exercise testing in healthy populations, as well as muscular fitness testing protocols and norms for children and adults.

9.ACSM’s Guidelines for Exercise Testing & Prescription-This critical handbook delivers scientifically based standards on exercise testing and prescription to the certification candidate, the professional, and the student. This manual gives succinct summaries of recommended procedures for exercise testing and exercise prescription in healthy and diseased patients New pre-exercise health screening recommendations are critical to helping more of the population begin a safe, healthy physical activity program without consulting a physician. New and expanded information on the risks of sedentary behavior, clinical exercise testing and interpretation, high intensity interval training, musculoskeletal injury risk, fitness testing protocols and norms, and an expansion of the principles of health behavior change are included. Additionally, significant reorganization of content will help you reach the information you need quickly. This manual is an essential resource for all exercise professionals, as well as other health professionals who may council patients on exercise including physicians, nurses, physician’s assistants, physical and occupational therapists, dieticians, and health care administrators.

10. NSPA (NATIONAL SPORTS PERFORMANCE ASSOCIATION) – CPDS(CERTIFIED PROGRAM DESIGN SPECIALIST)- this certification was created by renown strength & conditioning coach, Robert Dos Remedios.This is quite an in depth certification which teaches how to ensure that a coach could not only know where to find information they could trust on how to design their own effective programs, but to understand the science and logic behind why each choice throughout the program design process is being made. It’s a digital course and is completely online.

By earning this Certification, you will be educated on how to effectively design scientifically and ‘real world’ sound training programs to empower your athletes to reach their potential through:

• Understanding sound program design.
• Knowing, in-depth, the role periodization plays in effective programming.

• Having a compressive grasp of the importance of all essential
  programming components.

• Understanding what movements are essential cornerstones of good
  programs – and having a thorough exercise library to draw from.
• The ability to blend scientific principles with practical coaching applications.

On enrolment you get access to:

• The Program Design Specialist Certification Course
• 9 Core Modules and Video Lessons
• PowerPoint Handouts and Program Design Manual
• Workout Cards Plug & Play System
• Exercise Library – Over 130 Exercises
  

To know about the prices and other information on the course, log on to its official website.