| Titles | Order |
| Julius Knipl, Real Estate Photographer: Stories by Ben Katchor | Outstanding Graphic Novel or Collection, 1997 |
| Lost in the Alps by Cosey, | Outstanding Graphic Novel or Collection, 1997 |
| Frank Vol. 2 (Frank) by Jim Woodring | Outstanding Graphic Novel or Collection, 1998 |
| The Little Man: Short Strips, 1980-1995 by Chester Brown | Outstanding Graphic Novel or Collection, 1998 |
| The Hey Mister Celebrity Roast by Pete Sickman-Garner | Outstanding Graphic Novel or Collection, 1999 |
| Hicksville by Dylan Horrocks | Outstanding Graphic Novel or Collection, 1999 |
| Time Warp: The End of the Century Club by Ilya | Outstanding Graphic Novel or Collection, 1999 |
| Tiny Bubbles by James Kochalka | Outstanding Graphic Novel or Collection, 1999 |
| Clan Apis by Jay Hosler | Outstanding Graphic Novel or Collection, 2000 |
| Comix 2000 by L'Association | Outstanding Graphic Novel or Collection, 2000 |
| Drawn & Quarterly (Volume 3) by Chris Oliveros | Outstanding Graphic Novel or Collection, 2000 |
| New Hat Stories: Banks/Eubanks by Tom Hart | Outstanding Graphic Novel or Collection, 2000 |
| Box Office Poison by Alex Robinson | Outstanding Graphic Novel or Collection, 2001 |
| Jimmy Corrigan: The Smartest Kid on Earth by Chris Ware | Outstanding Graphic Novel or Collection, 2001 |
| Mail Order Bride by Mark Kalesniko | Outstanding Graphic Novel or Collection, 2001 |
| Safe Area Gorazde: The War in Eastern Bosnia 1992-1995 by Joe Sacco | Outstanding Graphic Novel or Collection, 2001 |
| Snake 'n' Bacon's Cartoon Cabaret by Michael Kupperman | Outstanding Graphic Novel or Collection, 2001 |
| Fallout by Jim Ottaviani | Outstanding Graphic Novel or Collection, 2002 |
| Haw! by Ivan Brunetti | Outstanding Graphic Novel or Collection, 2002 |
| Non #5 by Jordan Crane | Outstanding Graphic Novel or Collection, 2002 |
| The Summer of Love by Debbie Drechsler | Outstanding Graphic Novel or Collection, 2002 |
| Beg the Question (A Minimum Wage Collection) by Bob Fingerman | Outstanding Graphic Novel or Collection, 2003 |
| Epileptic by David B. | Outstanding Graphic Novel or Collection, 2003 |
| The Frank Book by Jim Woodring | Outstanding Graphic Novel or Collection, 2003 |
| Nightmare Alley by Spain Rodriguez | Outstanding Graphic Novel or Collection, 2003 |
| The Fixer: A Story from Sarajevo by Joe Sacco | Outstanding Graphic Novel or Collection, 2004 |
| Louis Riel: A Comic-Strip Biography by Chester Brown | Outstanding Graphic Novel or Collection, 2004 |
| McSweeney's Quarterly Concern No. 13 by Editors of McSweeney's | Outstanding Graphic Novel or Collection, 2004 |
| Teratoid Heights by Mat Brinkman | Outstanding Graphic Novel or Collection, 2004 |
| Above and Below: Two Stories of the American Frontier by James Sturm | Outstanding Anthology or Collection, 2005 |
| Bighead by Jeffrey Brown | Outstanding Graphic Novel, 2005 |
| Carnet De Voyage (Travel Journal) by Craig Thompson | Outstanding Graphic Novel, 2005 |
| Cinema Panopticum by Thomas Ott | Outstanding Graphic Novel, 2005 |
| Dead Herring Comics by Actus | Outstanding Anthology or Collection, 2005 |
| Fred the Clown by Roger Langridge | Outstanding Anthology or Collection, 2005 |
| Hutch Owen: Unmarketable by Tom Hart | Outstanding Anthology or Collection, 2005 |
| Why Are You Doing This? by Jason | Outstanding Graphic Novel, 2005 |
| Castle Waiting by Linda Medley | Outstanding Anthology or Collection, 2006 |
| The Clouds Above by Jordan Crane | Outstanding Graphic Novel, 2006 |
| Drawn & Quarterly Showcase: Book Three | Outstanding Anthology or Collection, 2006 |
| Fun Home: A Family Tragicomic by Alison Bechdel | Outstanding Graphic Novel, 2006 |
| The Push Man and Other Stories by Yoshihiro Tatsumi | Outstanding Anthology or Collection, 2006 |
| The Squirrel Mother by Megan Kelso | Outstanding Anthology or Collection, 2006 |
| The Ticking by Renee French | Outstanding Graphic Novel, 2006 |
| Wimbledon Green by Seth | Outstanding Graphic Novel, 2006 |
| Aya by Marguerite Abouet | Outstanding Graphic Novel, 2007 |
| Bookhunter by Jason Shiga | Outstanding Graphic Novel, 2007 |
| Drawn & Quarterly Showcase: Book Four (Drawn & Quarterly) by Chris Oliveros | Outstanding Anthology or Collection, 2007 |
| Exit Wounds by Rutu Modan | Outstanding Graphic Novel, 2007 |
| House by Josh Simmons | Outstanding Graphic Novel, 2007 |
| King-Cat Classix by John Porcellino | Outstanding Anthology or Collection, 2007 |
| Misery Loves Comedy by Ivan Brunetti | Outstanding Anthology or Collection, 2007 |
| Moomin: The Complete Tove Jansson Comic Strip - Book One by Tove Jansson | Outstanding Anthology or Collection, 2007 |
