My campaigns are all 3.5e with most Wizards (3.5e) supplements allowed. And a "Ask the DM" policy on using material from those supplements. I don't ban much, I just reserve the right to.
3e and 3.5e have some significant changes between them; most of which I forget about until I look at a 3e book and realise how bad some of the classes were (I'm looking at you, bard).
Really, you could use a 3e book with 3.5e without much problem (just as you could between 1e and 2e), but, for me, the major difference between 3.5e supplements and 3e supplements is that the designers had a much better handle on 3.5e design and didn't make as many mistakes - although they still make them from time to time.
Cheers!