I've long argued in favor of the artistic and literary merit of the graphic novel medium, although when I do so for the uninitiated, I USUALLY yield the balance of my time explaining the difference between comic books and graphic novels. However as with all mediums I am interested in getting my readers to enrich their lives by suggesting things you might not have heard of otherwise (you wait, I will eventually do a Missed Music) I figured I'd throw a few obscure graphic novel titles your way in the hopes that you might seek them out.
Y: The Last Man
I have never read a graphic novel that unseated the two best graphic novels I've ever read (The Sandman and Watchmen, respectively) from their seats, but I tell you, Y: The Last Man came as close as anything ever did.
The story is neatly encapsulated in it's title: An unexplained event kills all the male mammals on Earth, except an escape artist named Yorick (his sister is named Hero, which should make all you Shakespeare nuts giggle) and a capuchin named Ampersand. Together with a genetic scientist named Dr. Allison Mann and a government agent named 355 (that's three fifty five) they embark on a journey to find what caused the plague and figure out how to clone enough men to save the human race.
I know, I know, all of that sounds like there isn't much of a story in there, but there is and WHAT a story. Like all good sci-fi, the story looks deep inside it's post-apocalyptic setting to the intense humanity at it's center. Real and intelligent musings on the nature of the world and it's characters can make Y: The Last Man deeply affecting and often gut wrenching. It really is one of the best graphic novels ever published, so if you haven't read it, I recommend it even if you're not a fan of graphic novels.
Locke and Key
Best described as the result of HP Lovecraft and Stephen King having a kid and it being raised by Wes Craven (which is appropriate as it's written by Stephen King's son), this one is devoted to a family who moves across the country after the father of the family is murdered in a horrible accident, apparently not realizing that moving to a town called Lovecraft is probably the worst decision you could make under those circumstances.
From there it's a unique haunted house story, with fantastic art and a sensibility based in the darker aspects of the human soul. In many ways it's a closer cousin to Wes Craven's The Last House on the Left than Hellraiser, but that's only true to a point. If you've ever felt the need to seek out horror in mediums other than film, Locke and Key is a great place to start.
Also, quick side note: This one was tied for the list with an obscure series called Fall of Cthulu, but won out because you need an absurdly deep knowledge of Lovecraftian mythos to even begin to get into Fall. Still, if you have that grounding, it's unique and interesting, so if you thought that last sentence describes you, give it a glance.
Written by Brian Clevenger, late of 8-Bit Theater (which is STILL my favorite webcomic of all time), this one is essentially a science based, humorous cousin to BRPD (better known as Hellboy thanks to the movie). The story is devoted to a robot built by Nikola Tesla and his various adventures fighting everything from Rasputin, to Nazi Scientists to literal Lovecraftian horrors. I really can't describe it too well beyond that (comedy is hard to describe), except to say that the number of historical jokes borders on the absurd and it's well written and characterized (and regularly hysterically funny). This one can be kind of hard to track down, but trust me it's worth the effort.