- wrote an unused draft of X-Men (2000)
- Writer and creator of the comic book "Fray", published by Dark Horse comics.
- Wrote the song "Last Time" for Anthony Head's album "Music for Elevators" (2002)
- Wrote the song "Burn Me Down" for Amber Benson's film "Chance" (2003)
- Writes for Marvel's "Astonishing X-Men" series (2005-????). Graphic novels out so far (April 2007) are "Gifted", "Dangerous" and "Torn", but the next graphic novel "Unstoppable" is contracted and in the works. "Astonishing X-Men", recreated specifically for Whedon, has been one of Marvel's best-selling comics as of 2006 and was nominated for several Eisner Awards including Best Serialized Story, Best Continuing Series, Best New Series and Best Writer, winning the Best Continuing Series award in 2006. The storyline behind "Gifted" has been used for X- Men: The Last Stand (2006).
- Provided audio commentary for Innocence (1998)
- Audio commentary for City of... (1999) with David Greenwalt.
- Writer, "Runaways", Marvel Comics, (2007)
- Angel: After the Fall a.k.a Angel: Season 6 (with Brian Lynch ) (canonical continuation of the television show in comic book format by IDW Publishing) 12 issues. Writer/Editor
- Buffy the Vampire Slayer - Season 8 (canonical continuation of the television show in comic book format by Dark Horse Comics) Writer/Editor Issue #1: "The Long Way Home, Part 1" written by Joss Whedon, art by Georges Jeanty, March 14, 2007 Issue #2: "The Long Way Home, Part 2" written by Joss Whedon, art by Georges Jeanty, April 4, 2007 Issue #3: "The Long Way Home, Part 3" written by Joss Whedon, art by Georges Jeanty, May 2, 2007 Issue #4: "The Long Way Home, Part 4" written by Joss Whedon, art by Georges Jeanty, June 6, 2007 Issue #5: "The Chain" written by Joss Whedon, art by Paul Lee, July 25, 2007 Issue #10: "Anywhere But Here" written by Joss Whedon, art by Cliff Richards, January 2, 2008 Issue #11: "A Beautiful Sunset" written by Joss Whedon, art by Georges Jeanty, February 6, 2008 Issue #16 -19 "Time of Your Life" written by Joss Whedon and artist Karl Moline
- Angel: Long Night's Journey (comic book mini-series with Brett Matthews from Dark Horse Comics) Four issues.
- "Serenity: Those Left Behind" (three issues comic book mini-series-canonical continuation of television series "Firefly" and motion picture "Serenity"). -- Dark Horse Comics.
- Tales of the Slayers - (comic book anthology and canonical prequel of television/comic book series "Buffy the Vampire Slayer" and "Angel.") Dark Horse Comics Story: Prologue,Righteous, [edit] Tales
- Tales of the Vampire - (comic book anthology and canonical prequel of television/comic book series "Buffy the Vampire Slayer" and "Angel.") Dark Horse Comics Story: Tales of the Vampires,Stacy
- (2013) Comic Book, #DeadThings, Reese Riley, Corona Sky Productions/Dark Horse
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