I use the alternate death and dying rules, something like the weapon group rules, and something like one of the alternate Metamagic rules in my Mystara game. I also made the racial paragon classes available but so far nobody's bitten. (It also uses class-based defense bonuses and, to a very limited degree, armour as DR, but neither system much resembles its UA counterpart).
For the short-term Eberron game that's in the setup stage right now, I'm definitely using the gestalt character rules (may only have three players). I'm considering the spell point system, alternate death and dying rules, weapon group rules, and a different alternate metamagic system. I'll probably throw reputation and magic level in. I'd like some spells to have recovery times as per UA as well, but the characters probably won't get high-level enough for it to matter in this game.
Oh, and I'm open to most of the class variants, though I haven't had anyone actually use one yet. I have had them use similar variants of my own devising, if that counts (it's not from so much as inspired by UA).
EDIT - failed to mention Action Points, used in both games. Of course in the case of Eberron, they're core anyway.