Damn Al, you pretty much wiped out everything with that list
Let's start off with +1's:
GTO - This has levels of drama and pure emotion that's typically reserved for tragedies. And yes, it's a comedy series.
Ga-Rei Zero - I agree that you need to watch at least the first 3 episodes to understand what's going on.
Infinite Ryvius - Lord of the Flies in space!
Gonna -1 Baccano though. If you like character development and a cohesive story, don't watch this. Has the worst static 2D characters you'll ever see. Horribly stereotypical and completely over-the-top.
Now for my short list.
RahXephon - The music-inspired version of Evangelion. And to me, far superior to it.
Mawaru Penguindrum - Dark, quirky, often hilarious but always serious. (This is one series where you will have to essentially "rewind" and watch certain scenes twice. Once to see what the penguins are up to... and then again to pay attention to the more serious dialogue and story that's going on in the background)
Le Chavalier D'Eon - Honestly, I don't remember much about this series... just that it ended up pretty dark and pretty damn good!
Blue Gender - A mech series that is very much a hit-or-miss. Completely devoid of comedy. Filled with death and bloodshed, but at its core is a very solid romance. Characters have a ton of development, with very understandable reactions with regards to their environment.
