I'd say if you were running a homebrew campaign, stick with 3.0. You'll find the books cheaper (probably) and, at its core, it's still D&D. If you plan on using all kinds of new supplements, you might as well go 3.5... but whatever you do, don't lay them side-by-side and compare; you'll be sorely disappointed at the watering-down of 3.5 spells.
Example:
3.0 sleep; affects 2d4 HD of creatures, no save.
3.5 sleep; affects up to 4 HD of creatures, Will save negates.
And don't get me started on Sanctuary.