I personally like the idea of giving a level in a Prestige class as a reward, but I have only seen it mentioned once (at the end of Gamers 2, which is of course 3.5 not pathfinder).
And I can see some pretty obvious problems that need to be considered:
The player's not wanting levels in those classes, players not meeting the prerequisites, should the players be able to put more levels in that class after the reward, does it count towards the level cap of 20 (and therefore not letting them gain their final class ability)? The List goes on.
So my question to the Pathfinder Forums is can this be done, can I/how should I give levels in prestige classes to my players as a reward?
If your players want a Prestige Class, set it up so it's a "reward" right about the time they'd be entering it. Have them go on some sort of related in-game quest, and at the end they can take levels in it, needing to qualify as normal.
That's my opinion.
If they don't want any levels in any PrC, then don't even worry about it.
Symar's got it right. Unless they want PrCs, it's not much of a reward. Some in-game quest or initiation could be fun, if they want the class, anyway.
It would feel more special to know that they've earned the right to be part of a certain elite, rather than just saying "OK, you're 7th level now, so you can start your new class."
Of course, some players would be ok with just that.
I'm actually planning on doing that as part of an adventure I'm writing up. Certain (new and unique) feats and prestige classes are only available from certain NPCs, like a fencing trainer can teach the Duelist prestige class, etc.
I'm just not sure if a PrC is really a reward unless the character wants to build towards it in the first place.
Make sure though to talor them a bit though. You don't want to give your characters say.. The Duelist PrC as a reward, but then require all the requirements when they wern't building to it directly.
And if you do tell them about PrCs being rewards like this and they do build towards them, but you don't set up for the PrC they wanted.. Well thats bad too.
Its usually best to start frankenstiening PrCs for the PCs.. Gives it a bit more of a oooH factor when they are presented and able to go into with no real work other than the long and tedious quest that you set up before it.