Bizarro Episode: Intentional for the first few years. Every seventh episode or so was supposed to be weird.
Channel Hop: Sort of. The show had already been airing on Cartoon Network's late night slot for years, and when [adult swim] was made in 2001 to take over Cartoon Network's late night, they just didn't move it as it fit [adult swim]'s demographics. So it wasn't the show that moved, it was the channel that moved.
I Am Not Spock: Joel Hodgson is not pleased with Space Ghost confusing him with his character 'Joel Robinson'.
In Memoriam: "Sharrock," a tribute to musician Sonny Sharrock.
Keep Circulating the Tapes: In addition to the final six episodes, three episodes never made it onto DVD at all: "Self Help", "The Mask" (and its companion piece "Le Livre d'Histoire"), and "Gum, Disease". Also "A Space Ghost Christmas", which was never released to DVD in its entirety. Only two songs from the special made it. Also, the unedited versions of:
"The World Premiere Toon-In" (aka "President's Day Nightmare"): For copyright reasons, all the cartoons featured on the show were cut for the DVD release. Only the wraparounds are shown.
"Sleeper": A brief scene after the credits with Space Ghost, Zorak and Moltar in the commissary having ditched Slash on the set was removed.
"Explode": An announcement at the very end of episode from the late BBC DJ John Peel, stating that the Ghost Planet will now explode (hence the title of the episode...) was removed.
"Glen Campbell": The audio from The Simpsons clip at the beginning was removed, along with a line from Space Ghost ("Which one is Homer again? The baby?"), and an additional audio clip of Mr. Burns after the credits.
"Hipster": Sam Butera sings a portion of "Just a Gigolo", which was cut from the DVD and replaced with an original song.
"Joshua": William, The King of Imagination's brief appearance was cut for the DVD. Rumor is because Williams Street couldn't track him down to get him to allow his likeness to appear on home video.
"Cahill": Garrett Morris sings a portion of "For the Love of Money", which was cut from the DVD.
"Chambraigne": Al Roker was originally part of the Chambraigne commercial. He was replaced on the DVDs by George Lowe (though some would argue that was an improvement because... it's George freaking Lowe)
For a time, the unedited versions of the above (as well as the episodes not on DVD) could be obtained through the Adult Swim's "Create Your Custom DVD!" feature, but now that the Adult Swim Store has shut down, the only legal option is to buy the episodes via iTunes.
Speaking of the Adult Swim store shutting down, for a time it was impossible (aside from buying used copies online for outrageously inflated prices) to obtain Volumes 4 and 5, since they were Adult Swim Store exclusives. However, they have since been made available on iTunes with the rest of the series.
You can find the episode "The Mask" on the VHS release of that movie, which it was originally made for; it follows the film. (Or, you can just watch it on YouTube.)
Missing Episode: A special done for Mexican audiences during the 2002 FIFA World Cup where Space Ghost interviewed Mexican goalkeeper Oscar "El Conejo" Perez is apparently lost. The episode was unique because it was recorded in both English (with the original cast) and Spanish, yet Oscar Perez' lines remained in Spanish in both dubs.
There's also at least 12 missing episodes from the Gametap iteration.
Name's the Same: Seasons 3 and 4 each have an episode named "Switcheroo". Both have different premises.
Old Shame: To Mike Lazzo, who considers the show to be dead to him.
The Other Darrin: A variation: Gary Owens, the voice of Space Ghost in the original 1960s cartoon, is used by the current Space Ghost's former mentor, Warren, as a replicant so he could have Space Ghost on his own show. Gary is rendered as an image of Space Ghost over a boiling cauldron that occasionally blinks into his real face. The real Space Ghost, feeling that Warren violated their trust as mentor and student, confronts him and Gary to reclaim his identity.
In "Spanish Translation", Brak was voiced by C. Martin Croker. In all other appearances, he was voiced by Andy Merrill.
In "Woody Allen's Fall Project", Space Ghost was played by Andy Merrill, Zorak was played by Dave Willis, and Moltar was played by Gus Jordan.
Talking to Himself: C. Martin Croker voices Zorak and Moltar (though his voice was pitched down electronically for Moltar's lines).
Throw It In: Between takes, George Lowe was complaining about how some fruit baskets he bought around Christmas time were recieved by people at Cartoon Network. When putting the show together, they decided to use this bit during the intro for Fire Drill.
Trolling Creator: There's no way the uncut version of "Fire Ant" (that is, Space Ghost crawling after an ant for 10 minutes) could be seen as anything but this.
It also shows us a new future of rock 'n' roll dominated by Colonial-era musicians, who perform a bizarre cover of "Black Dog" with fast-food-related lyrics.
While it was in pre-production, HervéVillechaize was in negotiations to co-star as a sidekick of Space Ghost. Sadly, he killed himself before anything happened.
Certain bits of dialog in the initial draft of "Fire Ant" (as shown in "Table Read") were excised from the completed version, such as the flashback with Dr. Fishopolis; a different flashback to the old Space Ghost show; and a different opening line by Space Ghost: "Sorry I'm late. I was out saving your life... in the future!"
During Dragon*Con '99, it was revealed that The Tick was going to be a guest, but the fact that they couldn't find any good animation to use for the interview left the interview unmade.
There are two episodes that were announced that were never made, namely "One Way Out", and "Drop Out". One Way Out was going to feature Seth MacFarlane and Seth Green, but it was never made. Part of the Green interview was used for the beginning of an Aqua Teen Hunger Force episode.
"Snatch" began life as a completely different episode, "Dinner With Steven". It was featured on the 1998 season DVD as a bonus.
Writer Revolt: "Joshua" was the last episode written for the 1997 season, which was the longest season of the show. By this time, the writers were exhausted, so they didn't even bother to come up with a plot or do traditional interviews, and instead opted to write a series of sketches, with the motif tying it all together being a paid program starring Space Ghost. Despite their cranky mood (or perhaps because of it), "Joshua" ended up being one of the funniest episodes of the series, thanks to its Something Completely Different style, mixed with quite a bit of Self-Deprecation and Deconstructive Parody.