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