Alright, I've given in. 
I'm only going to list my very favorites, because I would never be able to prioritize and organize all of them. Or rather, I could, but it would end up taking me several hours of minute fiddling, because that's what my brain does. :|
1. Alistair He is one of my favorite fictional characters ever. Seriously, I could go on at great length about the reasons I love this fool as a character, and love his progression through Origins.
2. Anders I don't differentiate between Awakening and 2 (although I do get why people do). He, also, has a tremendous story arc, and I could go on about him as well.
3. Wynne I like her, I think, because I am like her, a bit, and I would put her on the list of fictional characters that I would like to have a beer with. 
4. Isabela I love that, to me, she is just so *real*. She's flawed, and damaged, but strong and capable.
5. Nathaniel Howe (At least today, he's number 5). I can't think of anyone I'd rather see as Commander of the Grey in Ferelden. Also, that bow.
(Now, there are only a couple of characters that I actively don't like, so if someone's not on this list, it's cuz this was my gut reaction, first five. Otherwise, as I said, I'd be here forever weighing options and all. *grin*)