Re: preserving knees and shoulders....
I agree completely that fitness is important for protection. Light to moderate weightlifting can be very useful, but don't overdo it as a muscle strain can open you up to injury on the mat. I also agree that proper ukemi technique is important. If you're having trouble with a roll or fall, ask your sensei or sempai for help. There are also some really great video resources out there. I like the Bruce Bookman two dvd series on ukemi myself. There are also a couple of really great clips on YouTube. Do a search on "Guido Ukemi" - not sure who Guido is but he has a great way of demonstrating good technique.
If you have a known injury, you might consider bracing or taping that area for extra protection. I had an ACL reconstruction a few years back, and wear a DonJoy Female Fourcepoint brace that was specificially designed for women. Some researchers debate whether it prevents injury or not, but I can tell you that it makes a huge difference in post-practice discomfort especially if we are in seiza alot. Also remember that you can mark an injured area with a bandanna or sticker to remind nage that you have an injury (though some people find it more helpful to mark the opposite limb...reverse psychology at play).
Lastly, the biggest injury risk factor in the dojo can often be pride. We're all a hard headed bunch of individuals, and it's really hard to sit on the sidelines with an injury. However, it is much better to sit out one practice to let a minor injury heal, rather than keep going and let it progress into something that will keep you out for months.