Do you mean the actual water pipe, where it gets dirty above the water line? If so, fill with water up to the line and then throw in a Denture cleaning tablet. Preferably an over night one (rather than a 3-5 minute one) and leaving it overnight.
If it's another part (stem, slider, diffuser, etc)... nothing I can really think of, other than just cleaning it on a regular basis
Throw the parts in a ziplock bag full of rubbing alcohol overnight.