I own a small handheld glass bong, and I change the water after each bowl, unless I am REALLY too wasted to get my arse off where it gets plonked, in which case, I change after the session.
I clean my bong with potassium or sodium methoxide in anhydrous methanol, it BURNS right through even the most baked on gunk, when I first used it, it was on my bong which had a thick film of brownish black gunk baked firmly on, and the solution cut through the filth like I just rinsed the chamber out with volcanic lava;D
I like to use NaOMe first, give it a water wash after the crap gets burnt off, then shake up with water/toothpaste to get rid of any smell, then fill with fresh water.
One neat trick, is to dissolve a couple of altoids or menthol crystals in the fresh water, so the smoke comes out nicely menthol flavoured.