I like being recommended media and enjoy recommending. Locke made a nice thread a while back that covered some enjoyable series, so I thought I'd throw done some others that I've enjoyed.
Berserk (ongoing) - top of the list and for a good reason. People will tell the the anime is good, but had a problematic ending. Skip the anime, go straight to the manga. This by far the best manga I've read, and can easily pull off the description "visual novel," without sounding ridiculous. Berserk is a dark fantasy manga that explores a variety of themes throughout its many arc with camaraderie, fate, and suffering topping the list. Guts, the main character very early on seems like a paragon of cliche. HE is brutish, wields a giant sword, seems nearly invincible in battle, and has a character design very similar to those found in the late 80s. In truth, he is acomplex individual coming to grips with the hand fate has dealt him while also attempting to break free of it. The art is richly detailed, the atmosphere is thick with melancholy, and the characters richly developed.
Hunter x Hunter (hiatus) - I found it to be a strangely alluring series. Many of its elements are very stereotypical shounen, and there are some early weak plot gaps you simply have to ignore--such as how whole contrivance and pomp of the hunter license. However, there are manyvery unique elements within the series that I found to be entirely redeeming. The main character, Gon, is entirely amoral without being any sort of anti-hero, which is odd for a very shounen series. There is also a fair amount of avoidance of fights in the series, because the enemies tend to be realistically superior and not merely something for the main characters to surpass. Key characters are at times discarded in the story; that is that the author develops them to a great extent and then decides to move on to something else and perhaps bring them back later. And perhaps the most intriguing elements are the very unique abilities possessed by the characters and the very unique situations in which they must use these abilities. The author is also incredibly detailed in developing his world. At one point he introduces a virtual reality game that involves cards, hundreds (perhaps it was one thousand cards?), and he explicitly designed and listed each one in his manga in an index section. Also the guy is married to the mangaka of Sailor Moon, making him even more of a hoss.
Eyeshield 21 (completed) - Perhaps one of the more entertaining sports manga. I found its most defining features to be very strong humor and genuinely clever plans by Hiruma. I also enjoyed how in a setting devoid of any magic or advanced technology the players are all given very unique and defining abilities.
Zetman (ongoing) - A new generation reconstruction of the superhero genre. If you enjoyed Marvel and DC comics about spider-man and superman like heroes, this is a story which has rebuilt what Marvel and DC are still in the process of deconstructing. Zet is a revitalized take on the traditional anti-hero, and his counter-part Alfaz is an exploration on the very old traditional superhero.
Liar Game (hiatus) - If you enjoy Death Note styles plots of continual one-upmanship and xanatos roulettes with xanatos roulettes, Liar game will be your fix. Perhaps not quite as strong as Death Note, but definitely enjoyable is you enjoy game thriller stories.
Shigurui (completed) - If you want gore, violence, and hatred, you'll find it here. Extremely graphic, Shigurui is a story of samurai portraying some of the most ruthless and despicable elements within a person. This is not Kenshin; this is not Samurai Champloo. I would say it's a horror story.