Good topic as this is what I am/was working on. Being as I have lower back problems I also have very tight hammy's. So when I got back to riding again I felt it was important to become more flexible as well as balanced. I bought the P90X workout program which is a non weight lifting program. I dont do all the workouts, rather I do the ones that offer what Im trying to improve. That said I do the Yoga, stretching, plyometrics, and core symetrics. I also do the legs and back routing in the base and off season period. The good news is I was gaining flexibility which was making the bike more comfortable. I was able to ride in a more aero position.
I also use a foam roller and occasionally a theracane. Ive found a softball also works well for the harder to reach stuff like the hip flexors.