- Samurai Jam (Slave Labor, 1993, tpb The Complete Samurai Jam, 176 pages, 2003, ISBN 0-943151-74-0)
- Skeleton Key (1995):
- Skeleton Key v1 : Beyond The Threshold (96 pages, Slave Labor, 2000, ISBN 0-943151-12-0)
- Skeleton Key v2 : The Celestial Calendar (198 pages, Slave Labor, 1999, ISBN 0-943151-15-5)
- Skeleton Key v3 : Telling Tales (96 pages, Slave Labor, 2001, ISBN 0-943151-13-9)
- Skeleton Key v4 : Cats and Dogs (104 pages, Slave Labor, 2000, ISBN 0-943151-19-8)
- Skeleton Key v5 : Roots (104 pages, Slave Labor, 2000, ISBN 0-943151-26-0)
- Negative Burn: “Skeleton Key: Bring on the Clouds” #44 (Caliber Comics, 1997)
- Dark Horse Presents:
- “Skeleton Key” (in Dark Horse Presents No. 126, Dark Horse, 1997)
- Annual 1998: “Skeleton Key: Witch” (Dark Horse, 1998)
- “Dead Love” (with pencils by David Perrin and inks by Sandu Florea, in Dark Horse Presents No. 141, Dark Horse, 1999, collected in Buffy the Vampire Slayer Omnibus volume 4)
- “Skeleton Key: Dead Can’t Dance” (in Dark Horse Presents vol. 2 #5, Dark Horse, 2011)
- “Skeleton Key: Room Service” (in Dark Horse Presents vol. 2 #6, Dark Horse, 2011)
- “Skeleton Key: Lost Property” (in Dark Horse Presents vol. 2 #7, Dark Horse, 2011)
- Buffy the Vampire Slayer #1–11, 13–15, 17–19 (Dark Horse, 1998–2000) collected as:
- Buffy the Vampire Slayer Omnibus volume 3 (328 pages, February 2008, ISBN1-59307-885-4) collects previous collections:
- Remaining Sunlight (collects #1–3)
- Uninvited Guests (collects #4–7)
- Buffy the Vampire Slayer Omnibus volume 4 (368 pages, May 2008, ISBN1-59307-968-0) collects previous collections:
- Bad Blood (collects #9-11)
- Crash Test Demons (collects #13–15)
- Pale Reflections (collects #17–19)
- Geisha (Oni, 1998, tpb The Complete Geisha, 2003, ISBN 1-929998-51-1)
- Aliens vs Predator: Xenogenesis (with pencils by Mel Rubi and inks by Mark Lipka and Norman Lee, 4-issue mini-series, Dark Horse, 1999)
- Breakfast After Noon (200 pages, Oni, 2000, ISBN 1-929998-14-7)
- X-Men Unlimited No. 30 (with Mike Lilly and Jim Mahfood, Marvel, 2000)
- Bizarro Comics (DC Comics, 240 pages, hardcover, 2001, ISBN1-56389-779-2, softcover, 2003, ISBN1-56389-958-2):
- “Wonder Girl vs Wonder Tot” (script, with art by Mark Crilley)
- “First Contact” (art, with script by Mark Crilley)
- “The One That Got Away” (in Star Wars Tales, Dark Horse, 2001, collected in Star Wars Tales volume 2, May 2002, Dark Horse, ISBN 1-56971-757-5, Titan Books, ISBN 1-84023-442-3)
- Slow News Day (160 pages, Slave Labor, 2001, ISBN 1-59362-080-2)
- Dumped (56 pages, Oni, 2002, ISBN 1-929998-41-4)
- Grendel: Red, White, & Black #2: “Devil’s Karma” (Dark Horse, 2002, tpb, 2005, ISBN 1-59307-201-5)
- Hellboy: Weird Tales #1: “Party Pooper” (Dark Horse, 2003, collected in Hellboy: Weird Tales volume 1, December 2003, ISBN 1-56971-622-6)
- Love Fights (2003):
- Love Fights vol 1 (168 pages, Oni, May 2004, ISBN 1-929998-86-4)
- Love Fights vol 2 (160 pages, Oni, January 2005, ISBN 1-929998-87-2)
- Namor (with co-author Bill Jemas, and pencils by Salvador Larroca and inks by Danny Miki, 12-issue series, Tsunami/Marvel, 2003)
- Kitsune Tales (with writer Woodrow Phoenix, 48 pages, Slave Labor, 2003, ISBN 0-943151-79-1)
- Little Star (176 pages, Oni, 2005, ISBN 1-932664-38-6)
- Paris (with art by Simon Gane, 5-issue limited series, Slave Labor, 2005–2006, tpb, 144 pages, August 2007, ISBN 1-59362-081-0)
- The Amazing Adventures of The Escapist #8: “Powder Burns” (Dark Horse, 2005)
- Put the Book Back on the Shelf: a Belle and Sebastian Anthology: “I Could Be Dreaming” (Image Comics, 2006)
- Clubbing (with Josh Howard, graphic novel, 176 pages, Minx, 2007, ISBN 1-4012-0370-1)
- Glister (3-issue mini-series, Image Comics, 2007, tpb, 64 pages, October 2007, ISBN 1-58240-884-X)
- Princess at Midnight (64 pages, graphic novel, Image Comics, 2008, ISBN 1-58240-928-5)
- 15 Love (with artist Tommy Ohtsuka, 3-issue mini-series, Marvel, 2011)
- Glister and the Haunted Teapot (64 pages, graphic novel, Walker Books, 2010 ISBN 978-1406320480)
- Glister and the House Hunt (80 pages, graphic novel, Walker Books, 2010, ISBN 978-1406320497)
- Glister and the Faerie Host (80 pages, graphic novel, Walker Books, 2010, ISBN 978-1406320503)
- Glister and the Family Tree (80 pages, graphic novel, Walker Books, 2011, ISBN 978-1406320510)
- Gum Girl: Catastrophe Calling! (64 pages, graphic novel, Walker Books, 2012, ISBN 978-1406329391)
- Gum Girl: The Tentacles of Doom! (64 pages, graphic novel, Walker Books, 2012, ISBN 978-1406329407)
- Gum Girl: Countdown to Destruction! (64 pages, graphic novel, Walker Books, 2013, ISBN 978-1406329414)
- Gum Girl: Music, Mischief and Mayhem! (64 pages, graphic novel, Walker Books, 2013, ISBN 978-1406329421)
- Princess Decomposia and Count Spatula (176 pages, graphic novel, Roaring Brook Press, 2015, ISBN 978-1-62672-149-4)
- Living Arrangements (152 pages, graphic novel—released only in French translation as Points de chute, Çà et Là, 2016, ISBN 978-2-36990-222-5)
- Glister (304 pages, graphic novel, Dark Horse comics, 2017, ISBN 1-50670-319-4, 978-1-50670-319-0)
- The Book Tour (272 pages, graphic novel, Top Shelf, 2020 in English (2019 in French), ISBN 978-1-60309-479-5)