Quote[/b] (savagebeast @ Oct. 10 2005,5:03)]goal220,
I've also been doing 5x5 and I had the same problem a few weeks ago with my shoulder hurting a bit from bench pressing. Also, my ankle and knees were starting to act up as well. For my shoulder, I just started doing some of the exercises from Eric Cressey's
Cracking the Rotator Cuff Conundrum. I don't follow sets, reps, or tempo schemes in the article, I just do 1 or 2 sets (that's total sets, not sets for each of the 4 lifts in the article) of 15 reps with a pretty light weight after I've finished the rest of my workout. So just pick an exercises from the article and do a set or two at the end of your workout. Sometimes, if I'm really drained at the end of the workout, I'll do a set or two at my place just using some light dumbbells instead.
And as far as sore knees and ankles, I started doing 1 set of both leg extensions and seated calf press at the end of my workout, using a really light weight and getting 15 reps.
Doing these few extra sets at the end of your workout doesn't take much out of you, and ever since I started I've had pretty much no more joint soreness.