Y The Last Man
Fables
Punisher MAX
Miracle Man
Batman vs Predator

I mostly only read Batman, so here are some others you should read if you're into him:

Long Halloween
Dark Victory
Death of the Family
Arkham Asylum - A Serious House on Serious Earth
Gotham Central
Batman and Robin (new 52)
...
Honestly there are a lot of good Batman storylines, just look up essential Batman and they're all pretty good.

Non-Batman:
Black Hole
Preacher
Sandman

Like A Velvet Glove Cast In Iron by Daniel Clowes (in fact any Clowes really, Wilson's really good)

If it has to be the super hero schtick then you could try Miracle Man by Alan Moore as Rockkkkkkk said. From Hell by Moore is really good as well, but is about Jack the Ripper.

If you have a tablet they make excellent comic book readers

Warning: You may not enjoy these at all

Transmetropolitan and Planetary are sort of amazing, Warren Ellis tells a great story.

The walking dead comics are fucking amazing. The story is also quite different from the show (they did that on purpose to avoid spoilers).

My cousin is really into comics. He has been getting into this new series called Trees. I've heard good things.

If you liked Watchmen I'd suggest V for Vendetta and League of Extraordinary Gentlemen, both also by Moore.

Seconding V for Vendetta if you're a fan of Watchmen. Most of my recommendations are already listed, but also seconding Arkham Asylum, Sandman, The Long Halloween. I also really like the Blacksad series, I feel the usage of animal heads really allows for some great expressions and it covers some pretty grim stories. I've also been reading IDW's MTMTE and RID Transformers series' but that's really only if you're into space adventure robot gore.

Other stuff including graphic novels:
Hellboy and BPRD
Maus
Thor: Blood Brothers

The entirety of scott snyders batman run is incredible (and greg capullo's art is probably my favorite), if you pick up the trade paper backs just be careful with the owl series though court of owls is #1 city of owls is #2 and night of owls is fill in issues from other characters that we didn't see in the main batman series. I get a lot of comics for the art and I don't really pretend to be the best at criticizing stories/writing as I haven't taken more than a few beginner creative writing classes but I don't think any of the comics on this list will have anything worse than a mediocre story (usually with imo incredible art)

Batman (vol 1-4, includes Court of Owls, City of Owls, Death of the Family, Zero Year - Secret City)

Planet Hulk - Super adventure based awesome story that I loved (the follow up world war hulk was kinda weak imo though)

Thor: God of Thunder (marvel now) (vol 1-2 The God Butcher, God Bomb) - I really can't emphasize how good these first two volumes are, which really surprised me since I've never really digged thor comics but they make it feel just absolutely epic in the greatest sense. If you like these you can feel free to pick up #3 The accursed, but I do think it kinda vreers a little in direction (though is still really good)

Allstar Superman - Just a great book, very classic

Uncanny Avengers - I'll admit this is probably the most likely for someone to disagree with but idk I liked avengers vs xmen and I think this was really cool follow up. Volume 1 is great, the next two volumes really vreer away from that storyline a lot though like everything that happens in volume 1 is just kinda like this huge plot device for the real story that happens in volumes 2 and 3

Batman and Superman - New 52 Vol.1 Crossworlds : I really like this series, the art is incredible and I really like the style of writing too.

I picked up New Avengers vol 1 Everything Dies recently and Captain america Trapped in Demension zone Z and I thought they were both aight, worth checking out and seeing if they get better (if you have to pick one new avengers was a bit better imo)

Superior spiderman's kinda cool but idk for some reason I just can't get behind it the same way a lot of other people do

Original sin started off really strong but it gets weird at the end, still worth picking up because it's changed a lot in the marvel verse

Avengers vs Xmen was an aight event, very action packed with some impressive panels

I've heard great things about xmen battle of the atom, that'll probably be the next thing I buy

Seconding batman long halloween and dark victory (great influential origin stories for a lot of batman characters) Y the last man and all hellboy ever

Got this for a friend of mine last Christmas

http://img2.imagesbn.com/p/9781595828699_p0_v2_s260x420.JPG

Also backing up V for Vendetta and Maus.

Preacher
Sandman
Savage Sword of Conan
Batman: Hush (was pretty cool)
Groo

Injustice: Gods Among Us

http://www.theaveragegamer.com/wp-content/uploads/2013/03/IMG_01551.png

I've never played the game, but the comics are amazing. Year Two is especially intense.

I also recommend sandman , I personally like saga and fables, saga is a little less hero/villain and more drama though

I read Sandman and Watchmen, but I mostly enjoy stuff from Bryan Lee O'Malley (Scott Pilgrim...)

love them