Bioware most definitely. I don't care about what hasn't gone as planned lately, such as DA2 and the paddling it's gotten from just about everyone, but they've made some of the best games I've ever played (KotOR, Jade Empire, DA:O, Mass Effect 1 and 2) and I adore their characters. The only series out of Square Enix that I've enjoyed was Kingdom Hearts, and I've never been able to get into Bethesda's games much (Tried Oblivion once, didn't like it) so based on who's games have impressed me the most, Bioware for the win. Personal opinion obviously.
And I think between Bioware and Bethesda, it all depends on what you want out of an RPG. Bioware goes more the route of a strong (if a bit linear) story and good character interactions with side quests being there if you so wish to pursue them. Bethesda goes for the open world style of gameplay, but I like that better in a sandbox like Prototype or something. I generally prefer story over open world, which is why Bioware is my choice. As for Square Enix, I don't really know enough about them to know their style. Yeah, I've played Kingdom Hearts, but that's really the tip of the iceberg for Square.