1) Farscape!!! - the best sci-fi show ever, once you get past the first half of Season 1 where they are doing the famaliar normal joe doesn't get alien ways to get you accustomed to the new universe. Once you get to the last 4 episodes of Season 1 you will see why it is the series I have rewatched 5 times over. Just seeing the main protaganist's transformation as a character from start to end is an amazing thing. Thats what I enjoy, every character starts as one thing and through interaction with each other and events, they change who they are. These are as close to living breathing people as you can get on the screen.
2) The Whedonverse (Angel, Buffy, Firefly, Dollhouse) - do I need to explain? (also in that order)
3) Terminator: TSCC - did what I never thought possible, make terminator into a relevant and thought provoking exploration of humanity and how far you would go to protect your family or the world.
4) Battlestar Galatica (all seasons were awesome, period)
5) Stargate Universe
6) Fringe
7) SG1
8) Eureka
9) Stargate Atlantis
10) The Star Treks (Voyager, DS9, TOS, TNG) - in that order
Yes I love torturted characters (my top 4). Thats why I love Sci-Fi because it allows you to explore characters and situations from much closer than would be normally possible do to the distancing effect of the fanatistical.
I just love serial storytelling and love characters that change throughout the show.
BTW don't know if it counts, since its fantasy, but Once Upon a Time is quickly becoming a new favorite.