As far as Batman goes, I would recommend The Killing Joke, Batman and the Monster Men, Batman and the Mad Monk, The Man Who Laughs and Arkham Asylum. I wasn't as enamoured with Year One and The Long Halloween, but they are pretty good. I would not recommend The Dark Knight Returns. It's pretty awful. (Carrie Kelly is awesome though)

Other than Batman, I would recommend Superman: Whatever Happened to the Man of Tomorrow?, Watchmen, and Swamp Thing. I enjoyed the first volume of Northlanders, but haven't picked up the rest. Also, formerly Known as the Justice League was pretty damn fun.

Quick edit: Also, I will second the Batman/Judge Dredd crossovers (though the collection is missing one of the stories, for some reason), and will nominate Hellboy.

Oh, forgot about Long Halloween very good imo. Like doccarnby, I can't really recommend much Frank Miller as he's kind of a lunatic who's never heard the word "subtle". I recommend picking up the book DC Universe: The Stories of Alan Moore. It contains all of Moore's DC work besides Swamp Thing, including Whatever Happened To The Man of Tomorrow? Just make sure you get the version with The Killing Joke.

I personally recommend:
Transmetropolitan
Watchmen
Looking for Group
The Dark Tower (graphic novel version)
Dawn of the Jedi (though only just started)
Freddy vs Jason vs Evil Dead
Discworld: Colour of Magic
Discworld: Light Fantastic
Spider-man Noir
The Goon
Trigun
Ghostbusters (IDW)
Giant Monster
Kingdom Come
Castlevania
and The Slayers

Also IF they ever make one, a graphic novel based on Good Omens, because the books is fantastic.

Johnny The Homocidal Maniac
Watchmen
Looking for Group
Superman Red Son

Y The Last Man
Transmetropolitan
V for Vendetta
I Am Legend
Sandman
The Boys (not sure if they finished this one)
Fables

Blacksad

Absolutely agree with both Preacher and Sandman. Wonderful work in both.

Sandman
From Hell
Honor Among Punks
Peter Bagge's "Buddy and Lisa" series
Locke & Key

This. To be honest though, i found The Walking Dead to be quite cliched. It could be intentional, but it detracted from the experience

I like Ex Machina and DMZ a lot.

Also, Josh Dysart's Unknown Soldier was really good, it was cancelled too early...

Thanks for the recommendations guys. Funny that so many of you mentioned The Dark Knight series, because that's the first thing that caught my eye when I was searching for comics on Comixology, and while I liked the art style a lot, I didn't know whether I should pick it up considering I don't collect Batman comics. I've always stayed away from DC comics because of so many branching story arcs, and with the Infinite Crisis branch, I think I just about gave it up.

I'm thinking of starting a hobby in collecting series of graphic novels, but I can't afford the ones with big story arcs, so I may get the popular ones like Batman/The Dark Knight in eBook format, while the more affordable series like The Walking Dead will be in physical copies. Out of all those recommendations mentioned, which ones (so far) have a clear start-to-end line, without having the authors change every now and then, with a reboot every few years? I know The Walking Dead does, but other than that ... ?

Watchmen. Seriously, it's the very definition of graphic novel. go get it. now.

@WBGhiro and other Watchmen promoters: thanks a lot! I'll be sure to get a copy of it from the library first.

Anyway just to plug for another project that I really like, Carbon Grey is really amazing. It's an example of a graphic novel where the level of violence is perfectly acceptable to me because it fits in with the theme. It's steampunk (I love steampunk!), it's grimdark without coming off as too overt, and the plot seems to leave the reader wanting more.

Because the author has reached $18K in his funding, he has released the first 3 issues of the graphic novel online. You can check them out here. I'm certainly not an art critic, but as someone who rarely reads graphic novels (I would mostly stick to certain DC/Dark Horse comics like Conan and Kull), I can't help but be impressed at how well elucidated the narrative is by the artistic style.

Issue #1
Issue #2
Issue #3

In no particular order.
-Watchmen
-Fables
-Atomic Robo
-League of Extraordinary Gentlemen
-Beanworld
-V for Vendetta

Out of these I recommended everyone take a look at Beanworld. It's just something I enjoyed a lot but don't ever really see mentioned, It deserves a little more attention.