I don't really have favorites, but the ones I usually recommend to people are:
Mawaru Penguindrum: The story starts off as a romantic-comedy (more comedy, less romance), but, as the story progresses, the show becomes underscored with a darker/more serious themes. (24 episodes)
Another: It's a short, well-paced horror story about a cursed classroom. The entire series is focused on the uncovering of this mystery and discovering how to rid the curse. (13 episodes)
As for the last one... Um, I don't really know. I have a few titles in mind, but I generally avoid suggesting long series (mainly because I also have trouble justifying why X title is 100+ episodes when it just gets sluggishly slow by 30....)....lol