I still play 3.5, when I run it it's mostly as-written (with a few Unearthed Arcana variants). Except for a few minor complaints (clunky weapon-size rules and some oddities in the spell lists and descriptions mostly) I think it's the best version of D&D ever made.
I really like d20 Modern and run and play it when I can, but that's not that often.
I'm personally really getting fond of Iron Heroes, and to me it will largely supplant D&D as my fantasy RPG of choice (although with another magic system, I don't care too much for the Arcanist).