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There's a lot of really good stuff out there (and another 90+% of horrible crap, but the good stuff is enough to keep you busy for a while):

Naver has been betting strong on infinite-canvas style, both eastern translated works and english-original ones (check the page out, there's A LOT of webcomics there, a bit of everything for everyone)

Girl Genius got most of the Hugo awards for graphic story in the first years of the category

uhm, I'm a bit busy at the moment so I'll just list a bunch of webcomics I liked below, if you look at what the authors of each of those recommend you'll find lots more, and these cover a fairly wide range of styles, themes and tones:

http://www.samandfuzzy.com/new...
http://www.johnnywander.com/
http://www.egscomics.com/
http://www.gunnerkrigg.com/
http://flipside.keenspot.com/
http://www.somethingpositive.n...
http://oglaf.com/latest/
http://www.happletea.com/
http://www.errantstory.com/

For those who have not read GK: The story (generally) follows the young Antimony through her arrival and schooling at Gunnerkrigg Court: a place that merges magic and technology. Nearby is the forest, populated by mythical creatures and gods (think Princess Mononoke). GK is a well told coming of age story between Antimony and her friends. At the same time GK is a beautifully rendered creation myth intertwining morality and the force of human belief.

Tom Siddell has masterfully crafted dozens of characters, each of which has a fully developed personality. Side characters reenter as necessary and provide a wonderful feeling of continuity and believability to the strip. The multiple storylines are distinct in tone and purpose but are never confusing, an issue many of the story based comics mentioned suffer from.

GK's tone shifts smoothly from childish fun (think the first 3 Harry Potter books) to dark examinations of natural and mystical philosophy. Its pantheon and art contains strong influences from Native American cultures and styles, such as the character of Coyote, but also others such as the Chinese Chang'e and the multicultural psychopomps. Tom manages to seamlessly integrate several art styles and mythos into a cohesive world. However, his world includes the mechanical (the heartbreaking story of the robots) and the natural, such as his crab couple inspired by eurypterids. Or this. http://www.gunnerkrigg.com/?p=688. When I wikipedia from GK, it could be to find out more about Muut or xiphosura.

For the overarching story, the intellectual challenge, and the smooth transition between art styles and tone, I put Gunnkrigg Court at the top.

1. Best overall: Schlock Mercenary
2. Funniest: Girl Genius
3. Best art: Gunnerkrigg Court
4. Most revelant: xkcd

Schlock has become a lot more kid-friendly since Tayler quit his job at Novell and now works surrounded by his children, but it's still entertaining. And he has kept its schedule for a pretty long time. Several other webcomics of that age gradually turned to weekday only, to Monday-Wednesday-Friday, to once weekly, but Schlock Mercenary keeps on updating every day.

Girl Genius has pretty good art, but what I like best is its large ensemble of delightfully inhuman characters. Every time I find a new favorite character, the Foglios introduce another crazy awesome character.

Gunnerkrigg Court doesn't have the very best art, but it's gradually getting better, and the story is intriguing.

xkcd is a comic by a nerd about nerds being nerdy.

While it lasted, Rusty and Co. (TVTropes) was consistently funny and had good art. The lawyers took it offline because of too many D&D references, particularly the author selling a plush doll of his Rusty character. I'm giving it extra credit for the YRO issue.

My runners-up for best overall comic would include Unsounded (first mentioned here -- mod up that comment if you agree), Gunnerkrigg Court (mentioned here), Magellan, Widdershins, and KiLA iLO.

And if nobody's mentioned it yet, TopWebComics is a site listing what webcomics are popular. Anybody can vote through a really simple captcha; you don't need to log in or anything.

For *funniest* web comic, Rusty and Co. made me laugh more than anything else. Runners-up are DMFA, Moron County, EGS, and Sluggy.

For *best art*, I would say it's A Redtail's Dream with Unsounded and Dresden Codak competing for second place, and a dark horse candidacy by Cucumber Quest for its uniquely cute art.

For the web comic *most relevant to me* as a reluctant hero space alien mad scientist vampire elf magical-sex-change victim, it's really hard to find a web comic that speaks to me, you know?

1) Best overall web comic series of 2012. (Any web comic that produced content in 2012): Gunnerkrigg Court is a brilliant webcomic that has a compelling plot, interesting characters and art that has developed superbly since the comic's beginnings.

2) Funniest web comic of 2012. (This one represents the single funniest comic of any web comic series.): Evil Inc. got the most laughs out of me this year, even if a lot of the humour was a bit Dad-joke-ish. Runners up would include: Penny Arcade , XKCD , Scandinavia and the World and Overcompensating .

3) Best art in a web comic of 2012. (Web comic from 2012 with the most amazing art ever): Dresden Codak is, without any doubt, the repository of some of the most geekiest and beautiful artwork the web has ever seen. Runners up would include: Namesake , Lackadaisy Cats , Sore Thumbs and Avengelyne

4) Web comic that was most relevant to you in 2012: Real Life , because his adventures with Harper are roughly mirroring my adventures with my daughter Hailey.

Honorable Mentions (because they'd likely win categories if there were a couple more here): Bad Machinery (Best Story), Eerie Cuties (Best Black & White), Three Panel Soul (Best Drama) and Wapsi Square (Best Main Character), and Sinfest (Lifetime Achievement) among others.

In no particular order I'm currently reading:
1) XKCD http://xkcd.org/ (and yes, 1110 was amazing art even though it's mostly about arcane, subtle or smart references)
2) Dilbert http://dilbert.com/fast (makes actual work seem a little less sad)
3) Lackadaisycats http://lackadaisycats.com/comic.php (guns, alcohol and cats)
4) Unsounded http://unsoundedcomic.com/ (thieves and their pesky offspring)
5) Gunnerkrigg Court http://gunnerkrigg.com/ (a school with mediums, shadows and robots)

I don't use RSS feeds for webcomics, so here is the set of pages I regularly visit:
XKCD We probably all know this one.
Cyanide and Happiness Somewhat twisted humour.
Errant Story Excellent art and storyline.
Bunny Strange humour about bunnies.
QC Indy rock comic of social interaction.
Megatokyo Megatokyo. Has gone downhill in recent years, but still good art.
Penny Arcade Gamer comic, quite famous.
PBF Perry Bible Fellowship hasn't updated in some time, but very funny when he does.
Edible Dirt is a series of single-panel jokes. Very funny, often somewhat twisted.
Ctrl-Alt-Del is a comic about a few gamer roomates.
LFG WoW/MMO/D&D spoof. Quite funny, good art, interesting plot. Many references break the 4th wall.
Two-Lumps is a comic about cats, 1 smart, 1 very, very dumb. I think the artist is stalking my cat to get ideas for the dumb one.
Gunnerkrigg Court Beautiful art, excellent story. And robots.
underpower hasn't updated in some time, great single-page art pieces recently and an actual story before.
Girl Genius is all about Mad Science.
Bunny System is a comic about psychotic rabbits.
Something Positive is very, very cynical. It actually has 5 webcomics on 1 page. Very much worth checking out.
Head Trip is... a head trip.
FLEM hasn't updated in a while, and has a strange and rather violent storyline. Back to single-panel shorts now.
VGCats video game cats is excellent, if you play video games.
Clan of the Cats Author is going blind, will continue if she gets better. Great story and art.
Dr. McNinja The adventures of Dr. McNinja. Clean art, good story, ninjas on fire.
Code Name: Hunter Magic/technology interaction in a world strangely dominated by talking animals. Excellent facial expressions, especially for being animals.
Awkward Zombie gamer comic similar to vgcats.
No Need for Bushido Samurai story, well drawn and reasonably well written.
Giant ITP hosts both The Order of The Stick, a D&D spoof, and The Battle For Gobwin Knob, a comic about a GM who gets sucked into a world of his own design, on the losing side of a no-win scenario.
Last Blood Zombies have taken over the earth and killed nearly all humans, so now the vampires fight to protect their dwindling food source. Excellent drawing and unique story.
Chopping Block Butch the serial killer. Sick, twisted humour, but very funny.
Dominic Deegan Oracle for Hire, is a good story with pretty good art.
The Traveling Gnome Great art, story seems good so far.
One-Liners may be offensive to some, or funny to those with a sense of humour.

note: I'm stealing descriptions from the wikipedia articles.

• Girl Genius [wp]- Girl Genius is a steampunk tale; "a gaslamp fantasy with adventure, romance and mad science", set in an alternate history "where the Industrial Revolution has become an all-out war" due to the appearance of "Sparks" -- highly charismatic mad scientists with supernormal abilities in one or more sciences.
• Gunnerkrigg Court [wp] - The comic details the strange events that surround protagonist Antimony Carver as she begins life at the foreboding, factory-like school complex of Gunnerkrigg Court.
• Lackadaisy [wp] - Lackadaisy (also known as Lackadaisy Cats) is a webcomic created by artist Tracy J. Butler, set in a Prohibition-era 1927 St. Louis inhabited by anthropomorphic cats. The plot chronicles the fortunes of the Lackadaisy Speakeasy after its founder is murdered.
• Dresden Codak [wp] - Described by the author as a "celebration of science, death and human folly," each comic generally focuses on a concept or theory from modern and postmodern philosophy, psychology, or science (particularly quantum physics)

ok, got tired of copy-pasting URL's and descriptions. just google theese, most of them have rss feed:

XKCD, Perry Bible Fellowship, Girl Genious, Gunnerkrigg Court, Templar, Arizona, Sinfest, Lackadaisy, The Broken Mirror, Saturday Morning Breakfast Cereal, Dinosaur Comics, Copper, Alpha Shade, Dresden Codak, The Curious Adventures of Aldus Maycombe, Inverloch, VGCats, Ctrl-Alt-Del, Questionable Content, Shortpacked!, Penny Arcade, The Book of Biff, Bunny, Contemplating Reiko, No Rest for the Wicked, The Devil's Panties, Girly, Penny and Aggie, Cool Cat Studio, The Adventures of Dr. McNinja, Johnny Saturn, 8 bit theatre, Nine Planets Without Intelligent Life, Zap! (zap in space), Mad About U, Ozy & Millie, Jack, Chugworth Academy, Marilith, Slightly Damned, The Awakened, Vampirates, Aether, Pinky TA, Orneryboy, Reman Mythology, Count Your Sheep, Errant Story, PowerPuff Girls Doujinshi (the one by bleedman), Everafter, Grim Tales from Down Below, Sugar Bits, Demonology 101, Zombies Calling, Ice, Brat-halla, The Phoenix Requiem, Last Blood, Flipside, Marry Me, No Pink Ponies, Shadowgirls, Purgatory Tower, El Goonish Shive, Badass Muthas!, Exiern, Xylia, A Girl and Her Fed, The BMovie Comic, Gone With the Blastwave, Candi, Flaky Pastry, Sorcery 101, Minus, Looking for group, North World, Nothing Better, Striptease, Handrawn Zoo, Rob and Elliot, Marsh Rocket, General Protection Fault, Rip and Teri, Maxwell the demon, Paradigm Shift, Fantasy Realms, Edwitch, The Unstuffed, Wayfarer's Moon, Undertow, Poultry Arisen!, God Mode, Kung Fool, Kill Harry, Pup

I can't guarantee you'll like them all, but I've read them all (most of them in all their extension) and I can assure that none of them make the eyes bleed (most of them are really good, in fact).

Also, an interesting indication of quality is the WCCA.