When I strated playing melodeon (not many weeks ago I have to admit!) I started to get a really stiff left shoulder, hands and elbows appear to be OK so far. Once I'd had how I was wearing the thing (straps were too long, in fact they didn't have enough holes in them to make them short enough for me) sorted out by my teacher the problems improved drastically, but I'd still agree frequent breaks are a good idea (stop and drink the tea you made instead of throwing it down the sink because you forgot about it through becoming engrossed in the music ;o).

Alexander technique has been mentioned, or you could try yoga for all sorts of RSI/hunched over computer typing/too much practicing type injuries, and you can calm your brain at the same time, it works for me!. I'd suggest a taught class rather than a video/book which could cause more harm than good if you're doing the postures incorrectly.