Given that the DMG states openly in plain black and white that even allowing Prestige Classes is completly up to the DM's discression, I'm a bit shocked to see negitive backlash against people who would ban even individual classes. Particuarly given how easy it is to pick out poorly balanced 'official' ones, since even the baic DMG prestige classes are clearly an option and and example...
Personaly, I have no problem with someone taking a prestige class simply for cool powers, since there's a certian set of good ones that are balanced primarly around their abilities, while having basicly no real flavor [at least as far as RP flavor]. The Devoted Defender, Lasher, and Assissian for instance, mesh well simply for their special abilities, and make sense as simply a way to make someone specialized.