I recommend:
V.B Rose:

Akuma to Love Song:

Keishichou Tokuhanka 007:

W-Juliet:

Kunisaki Izumo no Jijou:

and Komatta Toki ni wa Hoshi ni Kike:

Deadman Wonderland
It's really dark and sad. There's a lot of violence and sci-fi themes. But overall the characters are amazing and the art is nice. Warning- There is minor nudity, but nothing too too bad. And there's a lot of swears. But, it's just SO good! To me anyway...
Magnolia
First of all, it's a "gender bender" It could even be considered shounen-ai. It's really metaphorical if you think about it. It's a romance between the main character and like everybody. There's some suggestive scenes. But, it's kinda cute...

Acid Town
It's a soft yaoi. It's kinda disturbing... and it's about a male prostitute. There's romance in it as well was mystery and irony. I am in love with the artwork for it, too! It's just so... pretty.

Seven Days
It's a shounen-ai. It's so cute! I can't even stand it! It's romance, of course. The only thing that bothers me is that you never really know what happened at the end...

Dogs: Bullets and Carnage
I recommend reading Dogs: Prelude before this. But, anyway, it's so interesting. It's violent and creepy. (Haine is the best character ever) It can be funny and sad. But, it's mainly a manga about the mafia and evil scientists. It sounds stupid, but I recommend it! Again, there is a little bit of boob shots at some points, but it's actually important to the plot. Don't ask why, just read it...

Kuroshitsuji or Black Butler
There's loads of fanservice, but it has a weird plot. It's about demons and shinigami. There's shounen-ai undertones. The latest chapter nearly break the undertone barrier, but it's still a great manga. Again, violence....

Pandora Hearts
This manga is weird as hell. It's really sad, too. It hurts my head... But, I love it! Lots of Alice in Wonderland references. As well as plot twists.

Boys Next Door
It's so old and short! But, it's amazing! Honestly, my favorite yaoi! it's creepy and bloody! The main character's strange... and it's just so weird...

Loveless
There's only a handful of straight characters. It's very metaphorical. BTW keep in mind that there is NO age of consent in Japan.... And there are lots of cat boys... oh, and it's a shounen-ai

Skip Beat!!!!

AAA, B.O.D.Y., and black bird

Reborn!
Wandering Son
Nabari no ou

@samsam95: I liked your suggestions. Read one, bookmarked a few and even bought one off of amazon. ~.~

BLAME! \(^ ^)/
I'd say its... action/sci-fi. Its mostly about the artwork though, the mangaka Tsutomu Nihei was an architecture major before starting writing manga, and you can tell. The dialogue is sparse, cept for very ending which is a little wordy. Epic is the one word to describe it. Vast emptiness and an impossibly long journey.

Gokinjo Monogatari (Neighborhood Story), Paradise Kiss, and Nana. :3 I hold all shoujo to these golden standards.

! NARUTO!!!
2. Bleach
3. Ouran HIgh scool host club
4.DBZ
5. Id-entity
6. prince of tennis

Gintama, Gintama, Gintama.

and Nurarihyon no Mago.

I prefer either Papillion thats a good one or black bird that one is funny!!!!!

As far as quality, ongoing series go...

Not Equal - Ike Reibun(Simply amazing.)
Acid Town - Kyuugou(I think saying this is about a male prostitute is misleading. It's a very, very good series with a lot of heart)

They are both yaoi(though the only sex in acid town in the currently scanlated chapters is not like that, nor is it anything explicit). I wouldn't say they are unpopular though, just less well known than things like junjou romantica/etc.

As far as recommendations for great lesser known manga I'd have to start with 7 Seeds. Its josei manga, so its more mature than most shounen or shoujo titles. 7 seeds is a post-apocalyptic survival story with great characters and gripping plot. It isn't licensed as far as I know but you can find it on most scanlation sites. Its ongoing and the scanlations are a few volumes behind the Japanese release. Cannot recommend this enough.

I'd also recommend the Full Metal Panic manga. Its an adaptation of the light novels and follows the story long after the anime left off. Some of the novels, but not all, were translated and released by Tokyopop. Fan translations of all of them can be found online but they vary in quality. The manga follows the story pretty closely, so if you saw the anime and liked it enough to keep following the adventures of Sousake and Chidori check it out. Its ongoing.

Of the more action popular titles the ones I like the best are:
D. Grayman, Claymore, Black Butler, Blue Exorcist and Pandora Hearts

In the romance categories I'd say Maid-sama and Fruits Basket are popular for a reason, they are really good.

The World God Only Knows
Kaichou wa Maid-sama!

One Piece

Hana to Akuma

Pandora Hearts,

Bokura ga Ita

Ao Haru Ride

Samurai Deeper Kyo! Best manga ever.. mostly cause Hotaru is so awesome!!
Durarara!!
Zombie Loan! Zombies never looked so good!!
Aoi no Exorcist.. the manga is even better then the anime!!

King of Bandit Jing! It's quirky but I love it!