We have tinkered with a lot of house rules in my group, and here is what I have settled upon in my game:
(few of these rules do anything with numbers and other crunchy bits, as I get really tired of twinking and min/maxing the rules to the point that feels like powergaming)
1) Skill Focus provides two actual ranks of a skill, allowing a character to gain all benefits from a higher number of ranks than usual. (i.e. 1st level Bards may Inspire Competence, and characters might qualify for Prestige Classes earlier.)
2) Prestige Classes are not attainable by only meeting the game stat requirements; this is not a video game. Plot and role-playing developments are required. (i.e. You are a half-elf trying to be a Bladesinger? Read the Dragonlance novels and remember how much life sucked for Tanis as he tried to ingratiate himself into elven society.)
3) Don't bring your non-WotC feats, prestige classes, creatures, equipment, spells, etc to my Greyhawk game. There is certainly some good stuff out there, but there is a lot of crap, too. Instead of wasting my time trying to sort through the good and the bad, I stick to the basics. Besides, character concepts depend on good ideas, not a certain set of numbers and feats.
4) Power Components. I try to be very lenient with power components for casting spells and creating magical items. I strongly encourage spellcasters to take Item Creation Feats, because there are no Walmart MagicShoppes, and fandom/forgotten items of magical power are simply REALLY freakin rare! While major villains might have an item or two, you may very well expend more resources than you are gaining. Sure, sometimes you might be able to purchase one from an NPC, but he will charge at least 2-3 times the given "book price" because he ALSO knows how rare magical items are. Therefore, I try to provide plenty of opportunities for finding proper power components and "Item Formulas" so players may still work for and attain magical items at approximately the same standard rate the game is sorta balanced for.
5) Holistic's Fading Suns d20 has the concept of "Social Feats." I took it a bit further, allowing characters to use these "feats" to represent Guild Memberships, Reputations, Nobility, Church Ordination, Military Ranks, and other concepts that deal with lifestyle and occupation more than combat crunchiness. These are gained at 1st level and once every 5 levels after that. However, characters may "purchase" a Social feat for 500XP/character level (providing, of course, that plot and role-playing warrant it). I focus on these Social Feats to give better depth to characters, showing that many of them have occupations, responsibilities, etc. There is nothing more boring or insipid than the generic "homeless, wandering, treasure-grubbing, jobless-loser adventurer."