I think the biggest "problem" with 3e is the customization (with regards to Prestige Classes). Not trying to be critical, in many ways it outdid what many thought possible, but some things can only be seen from hindsight.
Take the barbarian for example. This class generally doesn't have issues with prcs. Why? Because they have interesting abilities to gain later by taking more barbarian levels, and they aren't hardwired to the class.
Spellcasting is pretty hardwired, it is usually considered the bulk of a class's power and if you take it away it becomes difficult to compensate. Imagine a barbarian prc where they did not gain BAB (or gained it at the wizard's rate). Not a pretty thought eh?
As far as spellcasters go, the druid and the wizard are the closest to the barbarian (for this discussion). They both have at least 2 good reasons to stay a druid or a wizard, things that prcs usually can't give, or can't give all of.
The cleric, sorceror, and bard are not as customizable as a hardwired feature (the druid also lacks the "customization" part, but it has the barbarian's "gain cool abilities by having more barbarian levels" ideal, with wildshape and thousand faces). This means that a sorceror doesn't have metamagic feats to lose by joining a prc, a cleric doesn't have any ability besides turning that they will lose by joining a prc (more on the cleric in a sec) and as long as the bard gets spellcasting and perform as a class skill, he's pretty golden.
There are mitigating factors for the bard and cleric. Both do not have the WORST BAB or the WORST HD. Clerics do have the WORST skill point/level, but bards do not. Prcs for clerics or bards should take this into account. If you are going to make a prc with clerics in mind and you wish to give cool abilities, full spellcasting, and full turning something has to give. And the cleric can give, she can give up her medium BAB, her good HD, or one of her good saves.
Then we come to the bastard of the 3e classes, the one which is altogether "new" to d&d, and unfortunately, the worst on the receiving end. There is 1 mitigating factor to remain a straight sorceror, and it is small (familiar abilities). You can't create a sorceor prc with a worse BAB than what he's got, its already the worst. Ditto HD, skill points/level, armor, everything. Hence, when designing a sorceror prc the ONLY THING you can penalize is spellcasting levels. Which, since the sorc was designed to be 1 level behind any other straight caster, puts him farther behind on his primary skill.
Anyway, to wrap this rambling up my point is this: If every class were designed with bonuses to look forward to at later levels, you would not see as many prcs being printed or chosen (although that depends on the group) for power-related reasons.
Here is a list of why you should stay in your base class (assuming the prc has similar base stats as the class you are leaving) [3.0]:
Barbarian: Uncanny Dodge, Greater Rage, DR, d12 HD
Bard: Good Skill list (heh)
Cleric: Turning
Druid: Wildshape, Venom Immunity, Thousand Faces, Eventually Immune Aging
Fighter: Feats, Feats, Feats (I think the fighter needs more "signature" feats like weapon spec)
Monk: the most reasons, but also the least amount of customization because all of those abilities are hardwired instead of chosen. OA rectified this a bit.
Paladin: Warhorse Abilities, Lay on Hands, Remove Disease (heh), Spellcasting
Ranger: Favored Enemy Bonuses, Spellcasting
Rogue: High level rogue abilities (hopefully a couple new ones in 3.5), sneak attack progression, uncanny dodge
Sorceror: Familiar advancement
Wizard: Familiar advancement, metamgic feats
The above list is not all-inclusive and with 3.5 coming out will hopefully be more evened out.
Technik