Let me give this a whack. If the stem is really brown, soak it in some hot water and oxyclean for about 20 minutes, then use a magic eraser and scrub off all the ugly brown. This isnt really harmful to the pipe as far as I know, I just think it looks nasty. Everclear dipped pipe cleaners inside the stem until no brown remains, salt and alcohol treatment as mentioned by others on the inside of the bowl, and I usually take a bristle cleaner dipped in everclear and scrub out the shank (the part where the stem fits into the pipe) until no gunk remains. Let it sit for a day or two and it should smoke like new.