Hey guys, let me tell you a little about myself, as I hope it will garner enough credibility that every athlete out there will heed my wisdom: I'm 32 and I'm in great physical shape (5'8" 173 lbs @ 8%bf). I wasn't always, though (used to be 245 @ 38% body fat). I'm a personal trainer, also. I was born with a left leg that is deformed. Two inches shorter than my right, only four toes, a foot only 85% the size of the right, and a ball-and-socket jointed ankle. Wicked, right? You should see how we lengthened it when I was 13! I've also torn my acl and underwent the reconstruction. A piece of my hamstring was harvested to replace the acl and my medial meniscus was torn and consequently removed. The right leg? It makes up for the left--Most guy at the gym wish they had two legs like my right--But then again, so do I!

So, you can see that I'm predisposed to a lot of imbalances. My hips aren't straight when I stand, my left arch doesn't exist, etc. This all causes chronic issues with my ankle, knee, hips, low back, and mid-back, and shoulders. I've uncovered plenty of tricks to keep my body in prime shape and free of injury while living a very active lifestyle.
I'm very flexible and I work very hard to train my body very holistically and with attention to fitness, not just weight, strength, etc. I can tell you that the acl reconstruction took me a year to work on my mobility, the rest of it all came before I decided to develop my flexibility (thanks to reading Eddie's first book a few years ago). At any rate, I recommend a number of things, so here goes:
First, get a good Sports Chiropractor who uses Applied Kinesiology and does extremity adjustments. get referrals from other athletes in your are who are please with their practitioner. I have an awesome guy in the n. atlanta area, if anyone needs him.
Make sure that your joints are lined up correctly. If they are not, you need to address structural and muscular imbalances causing that. This is where I find 90% of flexibility and mobility problems!
Train with stability exercises. Do resistance training. Strengthen muscles around weak joints. Yoga is great. If you're a beginner, go find Diamond Dallas Page's YRG (yoga for the regular guy) dvd or book. Awesome program. It'll kick your butt, too.
Myofascial release using a foam roller is critical, too.
Make sure your feet are correct--get orthotics if you need them--a weak foundation will make a weak structure.
Ice the joints when you have used them, even when they don't hurt. It's today's inflammation you don't feel that will be tomorrow's injury!
Practice proper [deep] breathing when stretching. Never stretch cold muscles or joints.
Finally, make sure that you control inflammation in your body by controlling your body's pH. Keeping alkaline by consuming lots of green leafy veggies on a regular basis (I prefer the juice thereof so that I don't bloat from the quantity) is the best way I've found.
If you can offer more information about what is tight (quads, hams, calf, glute, etc), I might be able to offer more specific advice/stretches/exercises. Can you be more specific about your injury? Good luck and I hope some of this helps.
And never forget....train with the gi on. Just kidding...
Jim