i don't read that much manga since i'm slow at reading them. plus, i usually tend to read those that are notably different from their anime adaptations. i'm one of those people who likes two different versions of the same story. but here are some that I like. there are a couple that i haven't read yet but plan on it once i finish other series.
1
Rozen Maiden (My personal favorite. Very different from the anime and very awesome. Especially the second series)
2
Fullmetal Alchemist (its worth watching both anime as well)
3.
Soul Eater (again follows a different story from the anime and still ongoing. Very intense now)
4
Arisa (great suspense. why can't it be an anime????)
5.
Rosario + Vampire (I HATE the anime. Fanservice is ridiculous and the suspense was toned down. read the manga. its way better)
6.
Gakuen Alice (looks can b very decieving. what started as a kid's school comedy got really dark)
7.
Fairy Tail (I'm new to this series. Decided to read after watching the entire first season in less than a week)
8.
Kitchen Princess (Drawn by Natsumi Ando, who did Arisa. This one is popular. I wonder if she doesn't want her work adapted)
9.
Shugo Chara (two good things about it. Heroine is a non-traditional magical girl lead and no filler)
10.
Pandora Hearts (This was recommended by a friend of mine. I haven't started reading yet but i will)
11.
Sailor Moon (i haven't read this one either but everyone should take a look since it had little in common with its anime)
I also want to mention. It's been announced that the Rozen Maiden anime will be getting another season

I'm so happy. I love the anime as well as the manga so i don't care what they plan to do with it as long as Kirakishou is in it. She's an important character and its sad that she only made a cameo in Traumend.