I used to have 2 problems in biking:
1. Right knee would nearly always hurt after riding - went to 2 different fitters, fitting didn't solve it.
2. Always felt a little awkward on the bike - weak core

The following things helped me personally a lot:

1. When I was working out, long story short I hurt my leg pretty bad, and ran across this warmup for working out which both healed my remaining injury (it wasn't healing on it's own after 3 months of being easy on it), and greatly increased my flexibility:

Defranco's Limber 11
Joe D's "Limber 11" (flexibility routine) - DeFranco's Training

2. I started doing one of those exercise videos. The one I have is "Shaun T's Rockin' Body DVD Workout" - it's kinda cheesy, but it's fairly cheap and got my whole body loosened up - and built up some core muscle which has made riding my bike WAY more comfortable.

3. I bought the book "Starting Strength" and started doing barbell squats. First couple times it made my knees hurt worse, but then I kept researching good form, got it down - and it make the annoying knee pain I had been dealing with for 10+ years when biking go away in a week. You don't need to do some crazy amount of weight, but do enough that you can feel it, and for me it got my knee muscles back into proper shape.

Seriously...I couldn't believe it, nothing else worked for the knee pain - not fitting, not stretching, etc, only retraining the knee muscles with good form and a large amount of weight suddenly magically made it go away.

Just my experience. I personally found the video from #1 far, far more helpful in increasing my flexibility on the bike than the static stretching I was doing before.