It seems almost impossible to compile a complete list of all the insanely awesome creator-owned books that combat the notion that comics are doomed to exist only as backwards-looking corporate cash grabs, but here's a start...
30 Days of Nights by Steve Niles and Ben Templesmith
100 Bullets by Brian Azzarrello and Eduardo Risso
100% by Paul Pope
Acme Novelty Library by Chris Ware
Age of Bronze by Eric Shanower
Alec by Eddie Campbell
America's Got Powers by Jonathan Ross and Bryan Hitch
America's Got Powers by Jonathan Ross and Bryan Hitch
American Born Chinese by Gene Yang
American Elf by James Kolchaka
American Flagg by Howard Chaykin
American Vampire by Scott Snyder and Rafael Albuquerque
Asterios Polyp by David Mazzuchelli
The Astounding Wolf-Man by Robert Kirkman and Jason Howard
The Astounding Wolf-Man by Robert Kirkman and Jason Howard
Astro City by Kurt Busiek, Brent Anderson and Alex Ross
Atlas by Dylan Horrocks
Bacchus by Eddie Campbell
Battlechasers by Joe Madureira
Battlechasers by Joe Madureira
Black Hole by Charles Burns
Blankets by Craig Thompson
Beanworld by Larry Marder
Beast by Marian Churchland
Beasts of Burden by Jill Thompson
Berlin by Jason Lutes
Black Kiss by Howard Chaykin
Blue Monday by Chynna Clugston
Body Bags by Jason Pearson
Bone by Jeff Smith
The Boys by Garth Ennis and Darick Robertson
The Boys by Garth Ennis and Darick Robertson
The Bulletpoof Coffin by David Hine and Shaky Kane
Captain Victory by Jack Kirby
Casanova by Matt Fraction, Gabriel Ba and Fabio Moon
Channel Zero by Brian Wood
Choker by Ben McCool and Ben Templesmith
Choker by Ben McCool and Ben Templesmith
Castle Waiting by Linda Medley
Cerebus by Dave Sim
Chew by John Layman and Rob Guillory
Codeflesh by Joe Casey and Charlie Adlard
The Coffin by Phil Hester and Mike Huddleston
The Coffin by Phil Hester and Mike Huddleston
Concrete by Paul Chadwick
Criminal by Ed Brubaker and Sean Philips
Crimson by Humberto Ramos and Brian Augustyn
Crimson by Humberto Ramos and Brian Augustyn
Daytrippers by Gabriel Ba and Fabio Moon
Demo by Brian Wood and Becky Cloonan
Deadenders by Ed Brubaker, Warren Pleece, Richard Case and Cameron Stewart
Deep Sleeper by Phil Hester and Mike Huddleston
Dreadstar by Jim Starlin
Deadenders by Ed Brubaker, Warren Pleece, Richard Case and Cameron Stewart
Deep Sleeper by Phil Hester and Mike Huddleston
Dreadstar by Jim Starlin
Echo by Terry Moore
Eightball by Daniel Clowes
Elephantmen by Richard Starkings, Axel Medellin, Möritat and many others
Elfquest by Richard and Wendy Pini
Empowered by Adam Warren
Essex County by Jeff Lemire
Ex Machina by Brian K. Vaughan and Tony Harris
Fables by Bill Willingham and Mark Buckingham
Fatale by Ed Brubaker and Sean Phillips
Fear Agent by Rick Remender and Tony Moore
Fell by Warren Ellis and Ben Templesmith
Finder by Carla Speed McNeil
The Filth by Grant Morrison and Chris Weston
Fortune and Glory by Brian Michael Bendis
Freak Angels by Warren Ellis and Paul Duffield
Freak Angels by Warren Ellis and Paul Duffield
From Hell by Alan Moore and Eddie Campbell
Fun Home by Alison Bechdel
G-Man by Chris Giarrusso
Girls by The Luna Brothers
Girls by The Luna Brothers
Give Me Liberty by Frank Miller and Dave Gibbons
Glamourpuss by Dave Sim
Glamourpuss by Dave Sim
Gødland by Joe Casey and Tom Scioli
Goldfish by Brian Michael Bendis
The Goon by Eric Powell
Grendel by Matt Wagner and many others
Groo the Wanderer by Mark Evanier and Serio Aragones
Grrl Scouts by Jim Mahfood
Habibi by Craig Thompson
Hark! A Vagrant Story by Kate Beaton
Hate by Peter Bagge
Hawaiian Dick by B. Clay Moore and Steven Griffin
Heavy Liquid by Paul Pope
Hell Yeah by Joe Keatinge and Andre Szymanowicz
Hell Yeah by Joe Keatinge and Andre Szymanowicz
Hellboy by Mike Mignola
Hilda and the Midnight Giant by Luke Pearson
Hilda and the Midnight Giant by Luke Pearson
I Kill Giants by Joe Kelly and Ken Niimura
The Interman by Jeff Parker
The Interman by Jeff Parker
Invincible by Robert Kirkman, Ryan Ottley and Cory Walker
The Invisibles by Grant Morrison, Steve Yeowell, Phil Jimenez and many others
It's a Good Life, If You Don't Weaken by Seth
iZombie by Chris Roberson and Michael Allred
Jetcat Clubhouse by Jay Stephens
Jetcat Clubhouse by Jay Stephens
Jinx by Brian Michael Bendis
Kabuki by David Mack
Kane by Paul Grist
Kick Ass by Mark Millar and John Romita, Jr.
Kill Shakespeare by Conor McCreery, Anthony Del Col and Andy Belanger
Kill Shakespeare by Conor McCreery, Anthony Del Col and Andy Belanger
Kill Your Boyfriend by Grant Morrison and Philip Bond
King City by Brandon Graham
La Perdida by Jessica Abel
Laika by Nick Abadzis
Last of the Independents by Matt Fraction and Kieron Dwyer
Leave It to Chance by James Robinson and Paul Smith
Leave It to Chance by James Robinson and Paul Smith
Liberty Meadows by Frank Cho
Local by Brian Wood and Ryan Kelly
Locke and Key by Joe Hill and Gabriel Rodrigeuz
Love and Rockets by Los Bros Hernandez
Lowlife by Ed Brubaker
Lowlife by Ed Brubaker
Madman by Michael Allred
Mage by Matt Wagner
Maus by Art Spiegleman
Maus by Art Spiegleman
The Manhattan Projects by Jonathan Hickman and Nick Pitarra
Midnight Nation by J. Michael Straczynski and Gary Frank
Ministry of Space by Warren Ellis and Chris Weston
Morning Glories by Nick Spencer, Joe Eisma and Rodin Esquejo
Mouse Guard by David Petersen
Mystery Society by Steve Niles and Fiona Staples
Near Death by Jay Faerber and Simone Guglielmini
Nemesis by Mark Millar and Steve McNiven
Next Men by John Byrne
Next Men by John Byrne
The Nightly News by Jonathan Hickman
The Nocturnals by Dan Brereton
normalman by Jim Valentino
Optic Nerve by Adrian Tomine
Orc Stain by James Stokoe
The Originals by Dave Gibbons
Palestine by Joe Sacco
Palestine by Joe Sacco
Pax Romana by Jonathan Hickman
Peepshow by Joe Matt
The Perhapanauts by Todd Dezago and Craig Rousseau
The Perhapanauts by Todd Dezago and Craig Rousseau
Persepolis by Marjane Satrapi
Phonogram by Kieron Gillen and Jamie McKelvie
Planetary by Warren Ellis and John Cassaday
Pop Gun War by Farel Dalrymple
Popbot by Ashley Wood
Powers by Brian Michael Bendis and Michael Avon Oeming
Popbot by Ashley Wood
Powers by Brian Michael Bendis and Michael Avon Oeming
Preacher by Garth Ennis and Steve Dillon
The Pride of Baghdad by Brian K. Vaughan and Niko Henrichon
The Pro by Garth Ennis, Jimmy Palmiotti and Amanda Conner
The Pride of Baghdad by Brian K. Vaughan and Niko Henrichon
The Pro by Garth Ennis, Jimmy Palmiotti and Amanda Conner
Promethea by Alan Moore and J.H. Williams III
Rachel Rising by Terry Moore
Queen & Country by Greg Rucka, Steve Rolston and many others
Queen & Country by Greg Rucka, Steve Rolston and many others
Rasl by Jeff Smith
A Red Mass for Mars by Jonathan Hickman and Ryan Bodenheim
The Red Wing by Jonathan Hickman and Nick Pitarra
Return of the Dapper Men by Jim McCann and Janet Lee
A Red Mass for Mars by Jonathan Hickman and Ryan Bodenheim
The Red Wing by Jonathan Hickman and Nick Pitarra
Return of the Dapper Men by Jim McCann and Janet Lee
Rocketo by Frank Espinosa
Rubber Blanket by David Mazzuchelli
Saga by Brian K. Vaughan and Fiona Staples
Salamander Dream by Hope Larson
Scalped by Jason Aaron and R.M Guéra
Savage Dragon by Erik Larsen
Scary Godmother by Jill Thompson
Scene of the Crime by Ed Brubaker and Michael Lark
Scene of the Crime by Ed Brubaker and Michael Lark
Scott Pilgrim by Bryan Lee O'Malley
Scooter Girl by Chynna Clugston
Scooter Girl by Chynna Clugston
Scud the Disposable Assassin by Rob Schrab
Secert Service by Mark Millar and Dave Gibbons
Shadoweyes by Ross Campbell
Sharknife by Corey Lewis
Sin City by Frank Miller
The Sixth Gun by Cullen Bunn and Brian Hurtt
Soul Kiss by Steven T. Seagle and Marco Cinello
Spawn by Todd McFarlane, Greg Capullo and many others
Spooked by Antony Johnston and Ross Campbell
Spooked by Antony Johnston and Ross Campbell
Strange Girl by Rick Remender, Eric Nguyen, Jerome Opena and many others
The Strange Talent of Luther Strode by Justin Jordan and Tradd Moore
Strangers In Paradise by Terry Moore
Strangers In Paradise by Terry Moore
Stray Bullets by David Lapham
Stumptown by Greg Rucka and Matthew Southworth
Super Dinosaur by Robert Kirkman and Jason Howard
Supercrooks by Mark Millar and Leinil Francis Yu
Supergod by Warren Ellis and Garrie Gastonny
Superior by Mark Millar and Leinil Francis Yu
Super Dinosaur by Robert Kirkman and Jason Howard
Supercrooks by Mark Millar and Leinil Francis Yu
Supergod by Warren Ellis and Garrie Gastonny
Superior by Mark Millar and Leinil Francis Yu
Supermarket by Brian Wood and Kristian Donaldson
Swallow Me Whole by Nate Powell
The Sword by The Luna Brothers
Tank Girl by Alan Martin, Jamie Hewlett and many others
Tellos by Todd Dezago and Mike Wieringo
The Sword by The Luna Brothers
Tank Girl by Alan Martin, Jamie Hewlett and many others
Tellos by Todd Dezago and Mike Wieringo
THB by Paul Pope
Three Days in Europe by Antony Johnston and Mike Hawthorne
Three Days in Europe by Antony Johnston and Mike Hawthorne
Torso by Brian Micahel Bendis and Mark Andreyko
Transhuman by Jonathan Hickman and J.M. Ringuet
Transhuman by Jonathan Hickman and J.M. Ringuet
Transmetropolitan by Warren Ellis and Darick Robertson
Turf by Jonathan Ross and Tommy Lee Edwards
Turf by Jonathan Ross and Tommy Lee Edwards
The Umbrella Academy by Gerard Way and Gabriel Ba
Ultra by The Luna Brothers
Usagai Yojimbo by Stan Sakai
V for Vendetta by Alan Moore and David Lloyd
The Walking Dead by Robert Kirkman, Charlie Adlard and Tony Moore
Wanted by Mark Millar and J.G. Jones
Wasteland by Antony Johnston and Christopher Mitten
Wasteland by Antony Johnston and Christopher Mitten
We3 by Grant Morrison and Frank Quitely
Wet Moon by Ross Campbell
Whiteout by Greg Rucka and Steve Lieber
Who Is Jake Ellis? by Nathan Edmondson and Tonci Zonjic
Wormwood: Gentleman Corpse by Ben Templesmith
Wormwood: Gentleman Corpse by Ben Templesmith
Y: The Last Man by Brian K. Vaughan and Pia Guerra
Zenith by Grant Morrison and Steve Yeowell
There are obviously tons of great things I'm forgetting, so if anyone wants to email me with titles to add, I'll try to update as I can.