These are my personal guidelines:
1) The campaign setting demands that some things be left out. Frex, in the archipelago game I'm currently (slowly) designing, the culture is an ahistorical mix of 18th-century guilds and late-Republic Roman political structures, with no concept of primogeniture,
et cetera et cetera ad nauseam. Therefore all feudal concepts are pretty much inappropriate; I've consequently excluded the paladin from the list of allowed base classes, because the feel of the class is very "holy-knight-in-shining-armour". Similarly, the island chain setting doesn't really suit elves and halflings, so I've excluded them as well.
2) Anything not inappropriate for the world or mechanically unbalanced is generally allowed. I like to adjust things rather than ban them outright for mechanical reasons; I'm less interested in taking the time to rework a class's flavour, for the simple reason that the d20 market offers a great deal of alternatives for most archetypes. For example, I'm allowing most of the non-spellcasting
Arcana Unearthed classes into the game; the champion ought to suffice for anyone who would like to play a paladin, as long as the feudal knight element of the paladin wasn't what attracted them to it.
Pretty much everything proceeds from these two axioms. For example, if I were to run a
Forgotten Realms campaign, I wouldn't hesitate to include material from products like Monte Cook's
Chaositech to spice up the antagonists or even the PCs, if that's the kind of game my players wanted. I aspire, as a GM, to make my world a playground for the PCs and the players, rather than for my own cool storylines and whatnot.
The best game I ever played was one where the PCs went nuts with their plots and goals, and it was ruined when the DM decided to end the game not by concluding the PCs' personal stories but by railroading the party towards his vision of a "cool" ending. I don't ever want to make that mistake, myself.
The only additional guideline I would impose is more of a metagame concern: I don't want to run a game where the party is doing something that one or more players isn't interested in or comfortable with. Frex, I wouldn't use
Book of Vile Darkness material if any one of my players objected, nor would I allow
Book of Exalted Deeds material if the party as a whole were not all interested in playing white-hat heroes (though they don't necessarily have to want to play an all-exalted party).
This doesn't mean that the players all have to agree on everything the party does in any given session - what plot threads they follow,
et cetera - but it
does mean that I want to give everyone in the group a fun and interesting time, since that's all I ever expect from a game myself.