One of my friends and former intern, Andrew Paul, has an article on EliteFTS that is a good read.
The Strength Coach’s Guide to Movement Assessment: Part 2
In the article Andrew goes over dysfunction in the lunge pattern and how to correct some of the area's that cause problems. The Thomas test is one of the tests that I utilize as well to check for hip flexor length on our athletes. It's a great indicator of several soft tissue issues that can be found in the hip. Coach Paul has been on my blog before and you can check out on of my previous posts on Andrew's article that also dealt with the hips here.
One thing that is important with the Thomas test is that I don't think Andrew mentioned is that the flexed leg is only flexed enough to eliminate compensation in the lumbar spine. The goal is to create a perfectly neutral spine and pelvic position. Often times coaches try to hug the leg to tightly to the chest. This causes a false positive for hip flexor tightness by causing the pelvis to rotate up towards the belly button. When this happens, the femur may not drop to parallel but in reality the hip flexor isn't tight, it's the posterior tilt of the pelvis compensating. Eliminating these compensations are highly important when doing manual muscle testing. Which leads me to my next point.
Check out the book Muscles: Testing and Function, with Posture and Pain by Kendall. This book is the authority when it comes to muscle tests in determining postural weaknesses, and dysfunction. It may be a little deep for some but if you are into any type of physical therapy, or are interested in muscle function / dysfunction then this book is a must read.