There's really only one villain in the Dragon Age series, in the traditional sense of an overarching antagonist acting against the protagonist with intent, and that's Loghain Mac Tir. Some of the origin stories have their own villains who affect the main story (Howe, Bhelen, Vaughan, perhaps Bharat), as do some of the sidequests in both games, but overall Dragon Age does a really neat job of not providing us with clear-cut heroes and villains -- even the PC can avert the hero trope, depending on what choices you make, and I would argue that Dragon Age 2 doesn't have a classic antagonist at all.
I find Loghain pretty interesting and very well written, but he's not my answer to this question. Instead, I'll pick someone with an even more ambiguous position on the hero vs. villain scale: Meredith Stannard.
To date, I haven't played a templar-supporing Hawke, only a fence-sitter and a mage supporter, so I've only related to Meredith as an antagonist. One of the reasons I'm keen on doing a pro-templar run is to get more insight into her character. Knight-Commander Meredith fascinates me. For nearly two thirds of the game, she's little more than a name, an unseen figure in the shadows, and yet she's the driving force behind so much that what happens in Kirkwall. It gives her a menacing quality that never quite disappears, even when she does finally make her entrance during the end of Act Three. Very effective, so interesting. She is a worthy antagonist, and I look forward to learning more about her as a sort of ally.
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