Man, no need to lay it on so thick.
Although I had a couple of stinkers in there (half-orc Favored of the Eye) I basically tried to balance prestige classes against the core classes.
There's a school of thought that prestige classes can be "better" than the core classes on account of the entry restrictions-- I don't subscribe to that school of thought. I do think, however, that entering the prestige class should require some sort of sacrifice or sub-optimal build on the way there; not because I want to justify making the prestige class "better" than the normal class, just so that it isn't a no-brainer to take the PrC and one of your core classes effectively disappears from the game.
Setting your entry requirements you should look at what class you expect PCs to enter from, and balance the PrC first against that expectation. Then you want to look at the requirements and shake them loose a little bit so that other classes could also qualify, with a little more work. For example, a class that you expect a rogue to be able to enter by 6th level might require four skills with 9 ranks each. As long as none of those skills are exclusive to rogues, then you also potentially open up the PrC to bards, rangers, barbarians, etc.
And, of course, I wouldn't make those four skills Hide, Move Silently, Search, and Spot. Every rogue is likely to have those, so you're not really setting a barrier to entry. Throw something sub-optimal or slightly off-type in there.
When it comes to actually balancing the nuts and bolts of the PrC, there are basically three "sliders" you have to work with: BAB, spellcasting progression, and skills. If you move any one of these sliders all the way up, the other two have to give. So that's what I balance first.
BAB is the easiest, and generally speaking, if BAB is high, so will the hit die be. Don't be fooled into thinking that you can "buy down" the HD to "buy up" something else. The HD just isn't "worth" enough. If the class has the full 1/1 BAB progression (+1, +2, +3) then give it a d10 and call it day. If it's 3/4, d8. If it's 1/2, d6 or d4.
Spellcasting has a couple of different components you can play with but the biggie is "+1 level of existing spellcaster class." That's top of the line. You can also give a prestige class its own, limited selection of spells-- WoTC does this all the time-- but I am not a fan of it. I hate the proliferation of alternate spellcasting lists. I hate having an Assassin list, a Blackguard list, etc. You should be able to do everything you need to do with the cleric, druid, wizard, ranger, and paladin lists. And the alternate lists are always so sub-optimal I almost never even use them, even as a player. I'd frankly rather have no spellcasting ability at all in a PrC and see the PrC get bumped up somewhere else.
Finally, I try to put some interesting feat-like ability in at every level of the prestige class, if I can. This is the most fun part and I think most folks have a pretty good idea how to balance these out. When in doubt, look at the core barbarian-- very well balanced class with something at every level. Remember that a "free feat" (such as the fighter gets) is more valuable than a "fixed progression" of abilities.
Hope that was useful!