Setting aside tobacco ('cos, let's be honest, no-one smokes tobacco with a bong, regardless of what head-shops say), there's also "legal highs" - synthetic cannabis analogues (K2/Spice/etc) and Salvia, for instance.

A lot of bongs are re-purposed chemistry apparatus, too. Not that having chemistry apparatus in your student flat is gonna look much better to a prospective employer than a bong. :P

Bongs can be used to smoke legal drugs, and there are a number of subtly different devices (like a shisha) for smoking tobacco.