As far as I can tell, this is the full list of those comics and creators who have won awards and those that have made the final ballots but haven't won since the first awards were given out in 2001. The format is alphabetical--it's the library clerk in me: I can't help it--so you have the name, then the year, then the number of awards won that year followed by the number of other categories the comic or creator was nominated in.
If that makes sense, skip this next part. If it doesn't make sense, here's Sinfest as an example. Its entry looks like this:
Sinfest: 2001--2, 0
2003--2, 3
2004--0, 3
2007--0, 2
2008--0, 1
That means it won 2 awards in 2001 and was nominated in no other categories except those 2. It got no nominations at all in 2002, then sprang back in 2003, winning 2 awards and being nominated in 3 other categories. In 2004, it won no awards but got 3 nominations; in 2005 and 2006, it again didn't make the final ballot in any category; but in 2007, it returned with 2 nominations and got 1 in 2008.
No comic has won an award or gotten a nomination in all 8 years though Megatokyo has received nominations in 7 of these years. As for who's won the most awards:
Mac Hall: 9
The Perry Bible Fellowship: 9
Chopping Block: 8
Penny Arcade: 8
Count Your Sheep: 7
Lackadaisy: 6
Questionable Content: 6
Also, since 2005, we've given awards to individual writers and artists for their bodies of work over the course of each year. Their names appear following the lists of webcomics.
I don't know if this is the most useful format for this information, but, well, here it all is.
Mike, the Registrar
Webcomics:
Award Winners
8-Bit Theatre: 2002--1, 4
2003--0, 1
Alpha Shade: 2004--0, 5
2005--3, 1
2006--1, 1
2007--0, 4
Angst Technology: 2001--0, 1
2002--1, 0
Anne Frank Conquers The Moon Nazis: 2003--1, 0
Applegeeks: 2006--1, 2
Astronaut Elementary: 2005--1, 0
Avalon: 2001--2, 0
2002--1, 2
Beaver & Steve: 2005--1, 0
2008--0, 1
Boxjam's Doodles: 2001--2, 3
Boy Meets Boy: 2001--0, 2
2002--0, 1
2003--1, 0
Chopping Block: 2001--4, 1
2002--4, 1
2003--0, 4
2006--0, 1
College Roomies from Hell: 2001--2, 2
2002--0, 5
2003--1, 1
2004--0, 1
2005--0, 1
Commander Kitty: 2003--1, 0
Cool Cat Studios: 2001--1, 0
Copper: 2005--0, 3
2006--1, 2
2007--2, 0
2008--1, 0
Count Your Sheep: 2004--6, 3
2005--1, 0
The Curious Adventures of Aldus Maycombe: 2007--1, 3
Demonology 101: 2003--2, 4
2004--2, 0
The Devil's Panties: 2005--1, 0
2006--1, 0
2007--0, 1
Dicebox: 2005--1, 2
Diesal Sweeties: 2001--0, 1
2002--1, 4
2003--0, 1
2008--0, 1
Digger: 2005--1, 2
2006--2, 0
2007--0, 2
2008--0, 1
Dinosaur Comics: 2005--1, 3
2006--0, 1
2007--0, 1
2008--0, 1
The Discovery of Spoons: 2005--1, 0
Dr. McNinja: 2007--1, 0
2008--0, 1
The Dreamer: 2008--0, 1
Dresden Codak: 2007--0, 1
2008--2, 2
Elf Life: 2001--1, 5
2003--0, 1
Elf Only Inn: 2003--0, 1
2004--1, 0
Errant Story: 2003--2, 2
2004--1, 0
2005--0, 1
Exploitation Now: 2001--1, 0
2002--1, 0
Fans!: 2001--0, 1
2002--0, 2
2003--1, 8
2004--0, 1
Five Ways To Love A Cockroach: 2006--1, 0
Freefall: 2001--1, 0
2002--0, 1
2005--0, 1
2006--0, 1
Girl Genius: 2006--1, 2
2007--1, 2
2008--2, 3
Goats: 2002--1, 1
2004--0, 1
The Green Avenger: 2006--1, 0
2007--0, 1
Gunnerkrigg Court: 2006--1, 3
2007--1, 3
2008--1, 6
Homestar Runner: 2003--1, 0
2004--1, 0
I Am A Rocket Builder: 2006--0, 1
2007--1, 0
Inverloch: 2005--1, 3
2006--1, 9
2007--1, 4
It's Walky!: 2002--1, 0
2003--1, 6
2004--0, 5
Jack: 2002--0, 2
2003--0, 3
2004--1, 0
2005--0, 2
Kevin & Kell: 2001--1, 0
2002--0, 1
Lackadaisy: 2007--3, 0
2008--3, 1
A Lesson is Learned but the Damage is Irreversable: 2005--1, 3
2006--2, 0
2007--0, 1
Mac Hall: 2002--2, 3
2003--4, 2
2004--3, 0
2005--0, 2
The Makeshift Miracle: 2002--1, 1
2003--0, 1
Megatokyo: 2001--0, 1
2002--4, 3
2003--1, 13
2004--0, 8
2005--0, 1
2006--0, 2
2007--0, 1
The Morning Improv: 2002--0, 1
2004--1, 0
Nine Planets Without Intelligent Life: 2006--1, 1
No Rest for the Wicked: 2006--0, 1
2007--1, 0
Nowhere Girl: 2003--4, 1
Octopus Pie: 2008--1, 2
The Order of the Stick: 2005--1, 1
2006--1, 2
2007--2, 0
2008--1, 1
Ornery Boy: 2004--0, 1
2005--1, 0
2007--0, 1
Ozy and Millie: 2002--1, 0
2003--0, 1
2004--0, 1
2005--0, 1
Penny Arcade: 2003--2, 10
2004--5, 3
2005--0, 5
2006--0, 1
2007--0, 2
2008--1, 2
The Perry Bible Fellowship: 2005--2, 0
2006--3, 0
2007--3, 0
2008--1, 2
PowerPuff Girls Doujinshi: 2005--2, 0
Pup: 2003--0, 2
2004--0, 1
2005--1, 0
PvP: 2001--0, 2
2003--0, 5
2004--0, 3
2005--0, 1
2007--1, 1
2008--0, 1
Questionable Content: 2004--0, 3
2005--1, 2
2006--1, 1
2007--4, 0
2008--0, 1
Real Life: 2001--1, 0
2003--1, 4
2004--1, 0
2005--1, 0
Reman Mythology: 2004--1, 3
2005--0, 5
Return to Sender: 2003--1, 0
2004--0, 1
RPG World: 2001--2, 1
2002--1, 2
2003--0, 7
Sabrina Online: 2001--1, 0
2002--0, 1
2003--0, 2
2004--0, 1
Saturday Morning Breakfast Cereal: 2003--0, 1
2006--1, 0
2007--1, 0
2008--0, 1
Saturnalia: 2003--0, 1
2004--1, 0
Scary-Go-Round: 2003--1, 3
2004--1, 6
2005--1, 2
2006--0, 2
2007--0, 2
2008--0, 1
Schlock Mercenary: 2001--1, 4
2002--0, 1
2003--1, 0
2004--1, 0
2005--0, 1
2007--0, 1
Sinfest: 2001--2, 0
2003--2, 3
2004--0, 3
2007--0, 2
2008--0, 1
Small Stories (Same Difference): 2003--1, 0
A Softer World: 2007--1, 0
2008--1, 0
Something Positive: 2002--0, 1
2003--0, 2
2004--0, 2
2005--1, 1
2006--1, 2
2007--0, 3
Sparkling Generation Valkyrie Yuuki: 2003--0, 1
2004--1, 0
2005--0, 1
2006--0, 1
The Sporkman Chronicles: 2001--1, 0
Star Cross'd Destiny: 2005--1, 0
Starslip Crisis: 2006--1, 4
2007--0, 3
Strings of Fate: 2003--1, 5
Supermegatopia: 2001--0, 1
2002--1, 0
2003--0, 1
2005--0, 1
Templar, Arizona: 2006--2, 3
2007--0, 3
2008--1, 1
Ugly Hill: 2006--1, 0
2007--0, 1
VG Cats: 2003--0, 1
2004--1, 3
2005--2, 2
2006--1, 1
2007--0, 3
2008--0, 1
Wapsi Square: 2004--1, 0
2005--0, 2
2006--0, 2
When I am King: 2002--1, 0
2003--0, 1
XKCD: 2008--1, 3
Zebra Girl: 2004--1, 0
2005--0, 1
2007--0, 1
Other Comics That Appeared on the Final Ballots
?: 2001--0, 2
1/0: 2001--0, 1
2002--0, 3
9th Elsewhere: 2004--0, 5
Achewood: 2004--0, 1
2005--0, 1
2006--0, 3
2008--0, 2
Acid Keg: 2005--0, 1
The Adventures of Captain Mooki: 2003--0, 1
Aki Alliance: 2006--0, 1
Alice: 2001--0, 1
Alien Loves Predator: 2007--0, 1
2008--0, 1
American Elf: 2003--0, 1
2004--0, 1
2005--0, 1
Angry D. Monkey: 2007--0, 2
Arrogance In Simplicity: 2001--0, 1
Ashfield: 2002--0, 2
Athena Voltaire: 2004--0, 1
Bang Barstal: 2006--0, 1
Bear and Kitten : 2008--0, 1
Between Two Worlds: 2007--0, 1
Biozoic: 2006--0, 2
Blotto Street: 2001--0, 2
Bobbins: 2002--0, 3
The Book of Biff: 2007--0, 1
2008--0, 1
Breakdown: 2007--0, 1
The Broken Mirror: 2007--0, 1
Bruno: 2001--0, 1
Bruno the Bandit: 2002--0, 1
Bunny: 2007--0, 1
2008--0, 1
Cascadia: 2003--0, 1
2004--0, 1
The Circle Weave: 2002--0, 1
2003--0, 1
Clan of the Cats: 2001--0, 3
2002--0, 2
2003--0, 2
The Class Menagerie: 2001--0, 2
2002--0, 1
Comicollage: 2001--0, 1
Contemplating Reiko: 2007--0, 1
Crimson Dark: 2007--0, 1
Crowfeathers: 2008--0, 2
Ctrl+Alt+Del: 2004--0, 1
2005--0, 2
Dan & Mab's Furry Adventures: 2005--0, 1
2007--0, 1
Daedalus Blue: 2006--0, 1
Dark Red: 2008--0, 1
Darken: 2007--0, 2
Detective Fork: 2005--0, 1
The Dreamland Chronicles: 2006--0, 4
2007--0, 2
2008--0, 2
Dueling Analogs: 2006--0, 2
Earthsong: 2005--0, 2
Eat the Roses: 2001--0, 2
2002--0, 1
2003--0, 1
E-Merl.com/Externality: 2003--0, 1 (for E-Merl in general)
2004--0, 2 (for Externality specifically)
2005--0, 1 (for Daniel Goodbrey)
2006--0, 2 (for E-Merl in general)
E-Sheep.com: 2003--0, 1
Estancia: 2006--0, 1
Evil, Inc.: 2007--0, 1
Fallen Angel Used Books: 2004--0, 1
Feral Calf: 2006--0, 2
Fetus-X: 2006--0, 4
2007--0, 2
Four Toon Tellers' Serial: 2001--0, 1
Framed!: 2001--0, 2
The Front: 2004--0, 1
2005--0, 1
Funny Farm: 2003--0, 1
Gaming Guardians: 2001--0, 2
2002--0, 2
2003--0, 1
General Protection Fault: 2001--0, 1
Girly: 2005--0, 1
2006--0, 1
2007--0, 1
Gluemeat: 2002--0, 1
Goats: 2004--0, 1
Gravity: 2001--0, 1
Green: Wicked Wicked Ways: 2005--0, 1
Grimbles: 2002--0, 1
Halfpixel: 2007--0, 1
Hereville: 2005--0, 1
Hero by Night Diaries: 2007--0, 1
Hold My Life: 2006--0, 1
IanComix: 2002--0, 1
It's About Girls: 2005--0, 1
The Japanese Beetle!: 2001--0, 1
The Journal Comic: 2002--0, 2
2003--0, 1
Junk Riot: 2006--0, 2
Kagerou: 2003--0, 3
Keaner.net: 2004--0, 1
Kid Radd: 2003--0, 1
Killroy and Tina: 2004--0, 1
2005--0, 1
Ko Fight Club: 2001--0, 2
Kung Fool: 2002--0, 1
2003--0, 1
Lang Lang: 2001--0, 1
Least I Could Do: 2007--0, 1
Legostar Galactica: 2007--0, 1
2008--0, 1
Life on Forbez: 2001--0, 1
Lords of Death and Life: 2007--0, 1
Magellan: 2005--0, 1
2006--0, 1
2007--0, 1
Magic Inkwell: 2003--0, 1
Man-Man Comics: 2002--0, 1
Melonpool: 2001--0, 2
2002--0, 1
2004--0, 1
2005--0, 1
Mike's Stupid Comic: 2004--0, 1
Minor Reality: 2001--0, 2
A Modest Destiny: 2003--0, 1
2004--0, 1
Narbonic: 2005--0, 1
2006--0, 1
2007--0, 1
Near the Delta: 2005--0, 1
Nerdz: 2001--0, 1
Normal Guy: 2001--0, 1
Nukees: 2001--0, 2
Odd Jobs: 2001--0, 5
Out There: 2007--0, 1
Outside the Box: 2003--0, 1
Outsider: 2002--0, 1
Overcompensating: 2006--0, 2
Parallel Dementia: 2006--0, 2
Partially Clips: 2006--0, 1
Penny and Aggie: 2006--0, 1
2007--0, 1
Pentasmal: 2001--0, 1
2002--0, 2
The Pet Professional: 2005--0, 1
The Phoenix Requiem: 2008--0, 9
Pictures for Sad Children: 2008--0, 1
Pirate and Alien: 2006--0, 1
Pokey the Penguin: 2002--0, 1
Psychic Dyslexia Institute: 2001--0, 2
Punks & Nerds: 2005--0, 1
Purple Pussy: 2004--0, 1
Queen of Wands: 2004--0, 1
The Realm of Atland: 2008--0, 3
Red String: 2004--0, 1
2005--0, 1
2006--0, 1
2007--0, 1
Reprographics: 2006--0, 1
Retail Weekly: 2001--0, 1
Riboflavin: 2002--0, 1
The Right Number: 2004--0, 1
Rogues of Clwyd-Rhan: 2001--0, 1
Sam and Fuzzy: 2004--0, 3
2005--0, 1
2006--0, 1
Savage Chickens: 2006--0, 1
2008--0, 1
Scrubs: 2001--0, 1
Secret of Mana Theatre: 2003--0, 1
2004--0, 1
Sheldon: 2007--0, 1
Shortpacked: 2006--0, 2
2007--0, 1
Silent Kimbly: 2007--0, 1
Sinister Bedfellows: 2007--0, 1
Skirting Danger: 2004--0, 2
2005--0, 1
Sluggy Freelance: 2001--0, 1
2003--0, 1
Smile: 2005--0, 1
2007--0, 1
Smithson: 2006--0, 2
Sock'd: 2006--0, 1
Sordid City Blues: 2006--0, 1
Sore Thumbs: 2004--0, 1
Spells & Whistles: 2004--0, 1
The Stiff: 2005--0, 1
Stuff Sucks: 2007--0, 2
Superosity: 2002--0, 1
Synchronicity: 2006--0, 1
Tales of the Traveling Gnome: 2007--0, 1
Talismen: 2007--0, 1
The Tenth Life of Pishio the Cat: 2005--0, 1
Three Panel Soul: 2008--0, 2
Today: the Comic: 2006--0, 2
Toothpaste for Dinner: 2006--0, 1
2007--0, 1
Triangle and Robert: 2001--0, 1
Trilokan: 2003--0, 1
Twisted Kaiju Theater: 2007--0, 1
2008--0, 1
Two Kinds: 2005--0, 1
Tymothi Godek: 2005--0, 1
Untitled Again: 2001--0, 1
Vicious Lies: 2001--0, 2
Vicious Souvenirs: 2003--0, 1
Wandering Ones: 2001--0, 1
The Weird Worlds of Pewfell Porfingles: 2002--0, 1
Weirdism: 2003--0, 1
Wendy: 2001--0, 1
What Birds Know: 2007--0, 1
Whimville: 2003--0, 1
White Ninja: 2006--0, 1
Wigu: 2004--0, 2
Wondermark: 2006--0, 1
2007--0, 1
Xenith: 2001--0, 1
You Damn Kid: 2004--0, 1
Zap!: 2006--0, 1
Zap Jones: 2001--0, 3
Zortic: 2001--0, 2
Writers & Artists:
Award Winners
Tracy J. Butler: 2007--1, 0
2008--1, 0
Shaenon K. Garrity: 2005--1, 0
2006--0, 1
2007--0, 1
David Hellman: 2005--0, 1
2006--1, 0
Kazu Kibuishi: 2005--1, 0
Phil & Kaja Foglio: 2008--1, 0
Ryan North: 2005--0, 1
2006--1, 0
2007--1, 0
Other Writers & Artists Who Have Appeared on the Final Ballots
John Allison: 2005--0, 1
2007--0, 1
Aimee Chow: 2007--0, 1
Aaron S. Diaz: 2008--0, 1
Sarah Ellerton: 2005--0, 1
2006--0, 2
2008--0, 2
Phil Foglio: 2008--0, 1
Nicholas Gurewitch: 2006--0, 1
2007--0, 1
2008--0, 1
Jerry Holkins: 2005--0, 1
Ian MacConville: 2005--0, 1
Michelle Mayo: 2006--0, 1
2007--0, 1
Dylan Meconis: 2008--0, 1
Chris Onstaad: 2005--0, 1
2006--0, 1
2008--0, 1
Tom Siddell: 2008--0, 1
Spike: 2008--0, 1
Kristofer Straub: 2006--0, 1
Matt Summers: 2007--0, 1
More Figures
2001: 24 categories, 115 nominees: 4.79 nominees per category on average
61 titles for an average of 1.89 nominations per title
2002: 22 categories, 88 nominees: 4 nominees per category on average
47 titles, 25 never before nominated, for an average of 1.87 nominations per title
2003: 29 categories, 163 nominees: 5.62 nominees per category on average
62 titles, 33 never before nominated, for an average of 2.63 nominations per title
2004: 27 categories, 119 nominees: 4.41 nominees per category on average
59 titles, 27 never before nominated, for an average of 2.02 nominations per title
2005: 26 categories, 115 nominees: 4.42 nominees per category on average
66 titles & creators, 32 never before nominated, an average of 1.74 nominations per name
2006: 27 categories, 134 total nominees: 4.96 nominees per category on average
67 titles & creators, 40 never before nominated, an average of 2 nominations per name
2007: 25 categories, 121 total nominees: 4.84 nominees per category on average
70 titles & creators, 33 never before nominated, an average of 1.73 nominations per name
2008: 18 categories, 91 total nominees: 5.06 nominees per category on average
49 titles & creators, 16 never before nominated, an average of 1.86 nominations per name