Deus Ex and it's not really close for me, unless you disqualify it because they're heavily RPG's.
Bioshock, though, I didn't find it particularly strong in gameplay. It had good gameplay, and had some neat powers. But it wasn't near as polished as half-life 2, or even call of duty (shooting mechanics wise). Nor the role playing elements of deus ex. But still, it's story and atmosphere more than made up for it.
Half life 2, I find a bit dated mechanically (except that it uses health packs instead auto regen hooray!). its still great no doubt. But it used to be one of my top 10 games, and it's fallen quite a bit after subsequent playthroughs (which all my top games go through).