My list basically consists of picking and choosing the "variants" from the DMG, picking which PrCs and expansion spells are used, banning Rangers (use Woodsman from WoT), and give Sorcerers 4 skill points.
A few others have come and gone, but the above are the staples.
Of course, the homebrew I'm setting up will be fairly radical. More of a d20 game than D&D: mostly new classes, change the magic system (prompting most of the class changes), modified monsters, custom races, etc.