About a year ago I was diagnosed with bursitis in my left shoulder... (though I think something may be tweaked with my rotator cuff) I will probably need to see a specialist somewhere down the line.
It hasn't affected my training TOO much... I just make sure to stretch and warmup well before working out. Occasionally I will lose a couple hours sleep due to the achy bastard, though...
I try to take a week completely off every three months of training or so. This seems to refresh the joints and get 'em ready for a little more abuse, lol! I'm sure most of us train through minor injuries and occasional aching backs, knees, wrists, etc...