First off, I'll say that I love the concept of prestige classes. When I decided to switch (from 1e, no less) it was one of the main attractions--the idea that you can gain special, rare, crazy, and interesting powers by virtue of membership in a prestigious group.
Obviously, like everything else in the game, PrCs have to be controlled by the DM, or else they become meaningless or downright silly.
Sometimes I start to feel a little PrC-burnout. There's so freaking many of them, and many are uninspired, ridiculously over- or underpowered, etc. But on the whole, I like the proliferation in books like Complete Warrior and Complete Divine. Personally, I usually prefer to tweak the class, or else design my own based on existing examples, to match the flavor of the character/group/campaign. But there are still a lot of times I look at a new PrC and immediately think, "How can I whip this into a villain to terrify my players...?
The only proviso I have is that I often feel that the flip-side of things are not being given their proper due. With a book like CW or CD, I'm getting cover to cover crunch; if I decide to pick it up it will be because that's what I'm looking for. But then, when I jaunt to the old FLGS for the newest FR book, it will be guaranteed to have 20-30 pages of PrCs. It gets frustrating at times to see pure-crunch books produced by WotC, but no books that are more than half flavor.