I like prestige classes as specialized classes, that are very good at something. I actually didn't like the variant multiclasses in Hyboria's F -series and would love to see such things dumped completely at 2 Ed. It would better, in my opinion, to replace them with prestige classes, especially because some of the variants are completely broken mechanically.
I think there are three strong points for prestige classes:
1) They give a distinctive feeling of speciality. Hyperborean Witchmen are much more unique if they have their own prestige class with their own little tricks instead of just being common scholars. Yes, you can customize characters with multiclassing and the choices you make concerning feats and spells... but it isn't the same thing.
2) They can be a source of social ambition for characters and player alike. When most prestige classes, such as in the case of sorcerous ones, are limited to a certain society, it add motivation from the part of game mechanics for a player character to belong to an organisation. It as well reinforces the feeling of secret covens and conspiracies knowing hidden things, which give them special powers. I like that - a hedge wizard should envy Lords of the Black Ring.
3) They add more variation and spirit to ways to create NPC's. This is strongly combined to first and second point. When I GM, I do enjoy building good stories and all that kind of things... but surprising players through pure game mechanics is kind of fun too. Obscure prestige classes give a chance to put against them opponents (both in social and violent situations) that baffle them with their exotic abilities. Yes, of course GMs could just pull stuff like that out of their asses - but I don't like being (too) arbitrary or risk breaking game balance.
