I had an excellent article on this written before my site crashed and I wish I had the heart to recreate it. The important thing is that I am a huge fan of stretching. Cycling is great for the body in many ways, but it is horrible for flexibility. One of my favorite quotes is “You know your a cyclist when standing up is considered stretching.” So in order to prevent injury and keep your body from becoming a tight ball, I suggest stretching as often as possible. I even work it into my day at work just to keep my muscles as loose as possible.
I think the key stretches are IT band related, calf, hamstring and back. For whatever reason the IT band stretch is the most often missing from many recommendations. It is surprising because it can be a big limiter on TT position and power applied. I recommend this move:
Here are several links to excellent sources on stretches you can do:
Pez (plus you have Daily Distractions)
Bicycling Mag (Yoga Based)