Some characters with a lot of prestige classes are overpowered. Some single-class characters are overpowered, too. Having more or fewer prestige classes says nothing about your overall power level, it’s all about which base and prestige classes.
So you can’t say something like, “oh, he’s got five prestige classes; he must be overpowered,” because that’s simply not true. You also can’t say, “single-classed? Must not be overpowered then!”
In fact, the prerequisites of prestige classes usually means its best to avoid taking too many, because prestige classes very often “tax” you for entry. Spending all your feats on weak things just to get into a bunch of prestige classes rarely works out in your favor. So when you say, “he’s got five prestige classes!” I’m thinking, “that was probably a mistake...”
But there are, of course, exceptions where it’s overpowered. But that’s very much the exception, and in such cases a character with just one of the prestige classes is still probably overpowered, just not as overpowered. Cases where individual prestige classes would be fine, but in combination there’s a problem are quite rare. It also happens, but literally only in a handful of cases, out of the stupidly-huge number of possible builds you can make in 3.x.
This can, by the way, be extended to multiclassing in general. Having levels in ten different classes doesn’t make you overpowered; it actually usually means you’re too scattered to be very much good at much of anything. And that’s assuming sane ways of calculating a multiclass character’s BAB and saves (i.e. Unearthed Arcana’s fractional BAB/save rules).
Also, for reference, very few people play with the multiclass XP penalty rules. They fail to accomplish what they ostensibly are supposed to do (discourage multiclassing), and their ostensible goal is widely seen as a bad idea in the first place (the breadth of material and relative ease of mixing and matching are two of the biggest strengths of 3.x). Also, groups with members at different XP values are a huge headache for DMs. So I wouldn’t factor that in much when comparing base classes and prestige classes. I cannot more strongly recommend against them; consider backporting Pathfinder’s Favored Class rules if it bothers you that without XP penalties Favored Classes are meaningless.