Well, in no particular order, my favorite.
- Warhammer 40k. It's so brutal and so demented, yet it never overpowers you and instead compels you to go deeper and deeper; the universe of 40k draws you in and invests you in fiction that has barely been tapped with its diversity and versatility.
Battlestar Galactica (re-imagined series). Took sci fi in a much more mature direction, moving away from all the Star Trek 're-hashes' that permeated sci fi, lumping the genre in with the 'geeks'. It also explores themes of faith and spirituality in a way that makes it relevant and insightful in a post-modern, cynical social milieu. It wasn't always consistent, but the series is easily one of the best.
Mass Effect - Bioware have created an extremely detailed universe in a short amount of time, that has a lot of depth and a lot of potential. It will be interesting to see how they explore it further in the future. It's mature, it's compelling and the Reapers are truly a terrifying idea. I like how it explores ideas of contemporary politics, racism, faith and humanity. A lot of the core themes and ideas may have been done to death before, but the Mass Effect universe does it well enough that it stands on its own and is excitingly fresh.
- Alien. Invasion/rape. Perversion. Corruption. Greed. All things which are idealistically 'alien' to human minds, yet so intimately related to. This is why the idea of the xenomorph is so terrifying and still stands the test of time. Not to mention the art which inspires Alien is some of the best and most thought provoking sexual art ever created.
- Bladerunner. I have an ambivalent relationship with the film. It asks many questions and never really answers any of them, then teases me with ideas and questions that aren't articulated in the film. It looks directly into the soul of humanity and no other fiction has managed to capture the raw emotion of human existence quite the way Ridly Scott did. It's dark, dirty, lonely, uncertain, strange and familiar. Yet, it has beauty and hope. Hallmarks of a masterpiece?