The last two anime series I watched were Magical Girl Lyrical Nanoha and Mai-Otome, and I'm hopeful that there's some similar manga out there. Basically - magical girls that deal with darker or stronger themes, or that are 'intense', preferably while also using the general lightness of the genre as a contrast/foil to this sort of thing. Narutaru falls within the scope of what I'm thinking as well, though it's not traditional magical girls. Demographics should probably be seinen or shounen, but if you think something in one of the others fits I'm happy to go with it.

(and yes, I read the Mai-Otome manga and it is terrible)

All of the manga here should fit your criterion.

Personally, I would recommend;
Soul Eater
Alive
Kobato
Bokurano (It's quite similar to Narutaru)
Black God
Fate/Stay Night
Taboo-Tattoo

Maybe Pretear. Note that the storyline of the anime and manga are different.
The same is true for Mai-HiME.


________________
If you've ever thought or said "Nice Guys finish last" and really meant it, then you should probably read this LJ post by DivaLion. It's incredibly insightful whether you're male or female.

From a bumper sticker I like:
"If you're gonna ride my ass, at least pull my hair."

Whoa, Revolutionary Girl Utena, definitely! You seriously haven't read it yet?
I liked the manga, but the anime is a lot darker and more psychological.
The Princess Tutu anime fits, too, as I hear. (The manga pretty much sucks, though.)