There is a bit of confusion regarding PrC's and the Tier system.  Here are a few guidelines....

#1) PrC's get a tier assignment by modifying an existing class's tier number.  PrC's are rated as -2, -1, 0, +1, or +2 tiers based on how much power and flexibility they add, and recalling how much you have to give up to get them.

#2) The DM is the final arbiter of how strong a PrC is with respect to a given build.

#3) PrC's -CAN- gestalt, but never with another PrC...onyl with base classes.

From the PrC Web Page:

Up Two or More Tiers.  These PrCs improve the power of their entry classes dramatically, either by building on strengths or by adding powerful new ones.  Expect characters with these to blow their single-classed peers out of the water (and possibly get DM-smote, depending on the base class's power).

Up One Tier.  These PrCs generally improve their entry classes substantially, without radically affecting game balance.  Expect characters with these to be powerful allies or dangerous enemies, without totally overshadowing their single-classed peers.

Even.  These PrCs are roughly on par with their entry classes overall, trading strengths in certain areas for strengths in others, or provides moderate gains for a moderate investment (ie required feats or unfavorable multiclassing).  Expect characters with these to fit naturally into a single-classed party.

Down One.  These PrCs are generally inferior to their obvious entry classes, losing out on important features in order to gain things that are likely not to matter in the long run.  Expect characters with these to struggle in a single-classed party.  They may still be viable for cherrypicking, or under heavy optimization.

Down Two or More Tiers.  These PrCs completely fail to do what they were trying to do, or makes heavy sacrifices for little to no gain.  Expect characters with these to be unplayable without heavy optimization effort, or some cunning trick.

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Next point of clarification:  A PrC is based on only one base class.  Choosing the base class that it relates to depends on several factors.

A) If the PrC adds spell casteing, it automatically modifies the spell-casting base class it is based from.

B) PrC is based off of the primary class, not the gestalt.  This is an important distinction.  Though a Fighter[Monk] may be mechanically identical to a Monk[Fighter], these are not the same classes, based on RP.

C) If two base classes might qualify, use the following :

Which Class has the most in common with this PrC?  For example, Shadowbane Inquisitor has elements of Rogue and Paladin, but the Paladin is clearly the "based-on" class.  If the PrC seems based off of a gestalt, first consider reversing class order.  Otherwise, don't gestalt the PrC.

LAAAAAAAAAAAAAAAAAAAAME. I was thinking of some pretty sweet prc-gestalt combos

That is all

If you're quoting from "the PrC web page", can you link to that page for our convenience?  Thanks for the post though; it does clear up a lot of stuff.

Links are in the gestalt system.  I've not fully implemented the PrC section, and I'm looking for good feedback on this.