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| Title | Original Air Date | Guests |
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| Spanish Translation | April 15 | Susan Powter, Kevin Meaney, The Bee Gees |
| Gilligan | April 22 | Bob Denver, Dawn Wells, Russell Johnson |
| Elevator | May 6 | Judy Tenuta, Timothy Leary, Ashley Judd |
| CHiPs | May 13 | Bill Carter, Joe Franklin |
| Bobcat | May 27 | Bobcat Goldthwait, The Ramones |
| Banjo | September 10 | Schooly D, "Weird Al" Yankovic |
| Punch | September 16 | Cindy Guyer, Jerky Boys, Dian Parkinson |
| Batmantis | September 30 | Adam West, Lee Meriwether, Eartha Kitt |
| Self Help | October 7 | Dr. Joyce Brothers, Rich Hall, Anka Radakovich |
| The Mask | November 4 | Jim Carrey, Charles Russell |
| Gum, Disease | November 11 | Branford Marsalis, Danny Bonaduce |
| A Space Ghost Christmas | December 25 | Council of Doom, Kevin Meaney |
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| Title | Original Air Date | Guests |
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| President's Day Nightmare | February 20 | Craig McCracken, Pat Ventura, Van Partible, Eugene Mattos, Genndy Tartakovsky, Dian Parkinson |
| 11 | Story Book | March 17 | Kirk the Storyteller, Carl the Cartoonist |
| 12 | Girlie Show | March 24 | Fran Drescher, Carol Channing, Alice Cooper |
| 14 | Hungry | March 31 | Michael Stipe, Lassie, Mujibur & Sirajul |
| 15 | Fire Drill | June 2 | David Byrne, Donny Osmond |
| 11a | Le Livre D'Histoire | June 9 | Jim Carrey, Charles Russell, James Kirkconnell, Carl Clark |
| 16 | Sleeper | July 28 | Hulk Hogan, Slash |
| 17 | Jerk | August 4 | Sandra Bernhard, B. Palmer Mills |
| 18 | Urges | October 20 | Matthew Sweet, Catherine Bach |
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| Title | Original Air Date | Guests |
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| 19 | Explode | February 2 | Terry Jones, Glen Phillips |
| 20 | $20.01 | February 9 | Joel Hodgson, Penn and Teller |
| 21 | Lovesick | February 14 | Carrot Top, Star Lady |
| 22 | Transcript | February 23 | Jonathan Richman |
| 23 | Sharrock | March 1 | Thurston Moore |
| 24 | Boo! | March 8 | Bill Nye, Michael Norman |
| 25 | Freak Show | May 22 | Wylie Gustafson, Bill Manspeaker (of Green Jell˙) |
| 26 | Switcheroo | June 5 | Susan Olsen, Elvira |
| 27 | Surprise | June 19 | Vinnie Dombroski, Jimmie Walker, Mike Watt, Dennis Diken, Pat DiNizio, Juliana Hatfield, Ben Folds, Cameron Diaz, Mark McEwen, Wes Johnson, Dr. Robert Bakker, Matt Talbott, Judy Tenuta, Lori Fetrick, Steve Henneberry, Method Man, Jill Cunniff, Rodney Trevon Oliver, Rev. Norbert St. Louis, Les Claypool, Larry Lalonde, Bobcat Goldthwait |
| 28 | Glen Campbell | October 9 | Matt Groening |
| 29 | Jacksonville | October 16 | James Hetfield, Kirk Hammett (of Metallica) |
| 30 | Late Show | October 23 | Janeane Garofolo, Dave Grohl, Flip Orley, John Popper |
| 31 | Cookout | December 11 | Emeril Lagasse, Nathalie Dupree, Martin Yan |
| 32 | Art Show | December 18 | Laurie Anderson, Stomp |
| 33 | Woody Allen's Fall Project | December 25 | James Kirkconnell |
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| Title | Original Air Date | Guests |
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| 34 | Rehearsal | July 18 | Fred Schneider |
| 35 | Gallagher | July 25 | Bob Odenkirk, David Cross |
| 36 | Edelweiss | August 1 | Beck |
| 37 | Anniversary | August 8 | Judy Tenuta, Bobcat Goldthwait |
| 38 | Zoltran | August 15 | Robin Leach, Merrill Markoe |
| 39 | Pilot | August 22 | Lori Fetrick, Steve Henneberry |
| 40 | Speck | August 29 | Jimmy Cliff, Jack Logan |
| 41 | Zorak | September 5 | Dr. Maxcy Nolan, Steve Arnold |
| 42 | Switcheroo | September 12 | Mark Hamill, Bill Mumy |
| 43 | Mayonnaise | September 19 | Jon Stewart |
| 44 | Brilliant Number One | September 26 | Peter Fonda, Buzz Aldrin |
| 45 | BooBooKitty | October 3 | Michael McKean, David Lander |
| 46 | Needledrop | October 10 | Ice-T, Ernie-C, Fred Willard |
| 47 | Sphinx | October 17 | Mike Judge, Harland Williams |
| 48 | Pavement | October 24 | Colin Quinn, Pavement, Red Green, Goldie Hawn, Tommy Davidson |
| 49 | Untitled | October 31 | George Clinton, Erik Estrada |
| 50 | Hipster | November 7 | The Millionaire, Sam Butera |
| 51 | Piledriver | November 14 | Rob Zombie, Raven Symone |
| 52 | Suckup | November 21 | John Henson, Bob Goen |
| 53 | Dam | December 5 | Charlton Heston |
| 54 | Boatshow | December 12 | Steve Allen, Andy Dick |
| 44b | Brilliant Number Two | December 14 | Peter Fonda, Buzz Aldrin |
| 55 | Telethon | December 19 | Bob Abdou, Pete Michael, Russ Powell |
| 56 | Dimethylpyrimidinol Bisulfite | December 26 | Pat Boone, Chuck D |
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| Title | Original Air Date | Guests |
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| 57 | Joshua | January 1 | Tony Bennett, Tom Arnold, Afro-Plane, Kathy Kinney, Ginny, the Dog Who Saves Cats, Paul Gilmartin, Annabelle Gurwitch, John Flansburgh, William, the King of Imagination, Ryah Rosenberg, Sean Medlock |
| 58 | Terminal | August 7 | Dr. Drew Pinsky, Marc Weiner |
| 59 | Toast | August 14 | Merrill Markoe, Adam Carolla |
| 60 | Lawsuit | August 21 | Greta Van Susteren |
| 61 | Cahill | August 28 | Garrett Morris, Mark McEwen |
| 62 | Warren | September 4 | Gary Owens |
| 62 | Warren (short version) | September 6 | Gary Owens |
| 63 | Chinatown | September 11 | Tyra Banks, Rebecca Romijn |
| 64 | Rio Ghosto | September 18 | Ben Stiller, Kevin Smith, Jim Jarmusch |
| 65 | Pal Joey | September 25 | Michael Moore |
| 66 | Curses | November 27 | Moby, Emo Philips, Shirley Manson |
| 67 | Intense Patriotism | December 4 | Jeff Foxworthy |
| Waiting for Edward | December 25 | Denis Leary |
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| Title | Original Air Date | Guests |
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| Chambraigne | October 8 | Bob Costas, Al Roker |
| Snatch | October 15 | Steven Wright |
| Girl Hair | October 22 | Hanson |
| Sequel | October 29 | Captain & Tennille |
| Curling Flower Space | November 19 | Jerry Springer, Sarah Jessica Parker |
| Table Read | December 3 | C. Martin Croker, George Lowe, Mike Lazzo, Dave Willis, Jim Fortier, Matt Maiellaro, Mark Banker |
| Fire Ant | December 10 | Conan O'Brien |
| King Dead | December 17 | Jon Benjamin |
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| Title | Original Air Date | Guests |
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| Fire Ant (short version) | January 3 | Conan O'Brien |
| Snatch (alternate ending) | January 28 | Steven Wright |
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| Title | Original Air Date | Guests |
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| Kentucky Nightmare | May 7 | Willie Nelson |
| The Justice Hole | July 22 | Dave Thomas |
| Knifin' Around | September 2 | Björk, Thom Yorke |
| Flipmode | October 14 | Busta Rhymes |
| Sweet For Brak | November 18 | Tenacious D |
| Mommentary | December 30 | Harriet Lazzo, Rachel Maiellaro, Sharon Willis |
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| Title | Original Air Date | Guests |
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| Mommentary - Creator's Commentary | May 12 | Mike Lazzo, Matt Maiellaro, Dave Willis |
| Mommentary - Jelly Bean | May 12 | Mike Lazzo, Matt Maiellaro, Dave Willis |
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| Title | Original Air Date | Guests |
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| Baffler Meal | January 1 | Willie Nelson |
| Whipping Post | November 23 | Dennis Miller |
| Eat a Peach | November 30 | Todd Barry |
| In Memory of Elizabeth Reed | December 7 | William Shatner |
| Idlewild South | December 14 | Jeff Probst |
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| Title | Original Air Date | Guests |
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| Dreams | January 11 | Triumph The Insult Comic Dog |
| Live at the Fillmore | April 12 | Susan Powter |
