I mentioned a Qigong book in another thread and it had a lot of good ideas on taking care of ligaments, massage being one good one. I've had a few pretty good injuries over the years and I've found that stretching, massage, and proper exercising of the area in particular are extremely beneficial! Gotta love being young with a healthy disrespect for gravity

-left shoulder, I snapped a pole vault pole at full bend and it hit me in the shoulder blade my senior year of hs...also, same shoulder, few years later, I was doing some military presses by myself and accidentally threw the bar over the supports at the end of my set (with 135 on the bar...) anyway, I've been doing lots of stretching, massage, pullups, dips, etc and that seems to have worked pretty well in keeping everything in good working order.
-right shoulder I drove a ski into after losing my balance while doing a heli 7-8 years back...I cant really even tell if its messed up or not, I've given it the same care of the left and its so much better! I think that same year or the year after, I hit a tree while skiing, although it was in such a manner that I took the impact squarely in the chest and only got the wind knocked out of me (after a quick upside down and backwards flight!) I havent skied in a few years, but that's been more because of time, money & priorities. I still long for the big mogul runs!
-blew out my L5 disc 10 years ago, that was from a combination of things...that is really NOT something I massage though, that is more core exercises combined with 2, 3 times a day stretching. I am a mess if I dont!
-I dont know how many times I've landed on my head over the years. I keep my neck stretched well and I also do moderate weight training with this cool head strap I got from ironmind. Massage works great there!
-dislocated my left index finger a couple years ago right at the metacarpal/falanges joint from a 9000 mph football that could have passed for a duck flapping its wings. I can still feel pieces in my finger from that, although I've stretched and worked that to a point where its pretty much back to normal. At least I can still grip a drumstick properly! Massage works ok there..
-knees? 2 words: osgood schlatter! bike is a godsend!
Basically, the most simple & rudimentary exercises will help strengthen your tendons & ligaments, the weight training helps the muscles. Be patient and work slowly, dont try and get back to 100% before your body tells you it is. And even then, with a lot of injuries, it will be right there to haunt you if you dont respect it. There's a right amount of exercise, rest, and massaging that will work for whatever the body part is that will get it working its best! Granted, sometimes parts of the injury will be permanent and you will be limited as to the amount of recovery...but if you keep at it and do things properly, you should be able to have your functionality at an acceptable level!