The TvTomeAdventures movie is gone. The site which the entire series was original hosted on has been dead for a long time, and the only person known to have recovered The Movie, Tails Clock, has experienced some...er...problems with his site as of late. The only place left to host the series at all at this point is Chris Niosi's newgrounds page, and if anything were to happen to that...
The credits, bloopers, and other material not uploaded to newgrounds is gone as well.
Web cartoon Bonus Stage never had an Episode 4 - Ep 4 being a number of previews for the artist's other works that was eventually removed. But one day, a "Lost Episode" was hidden behind a fake Internet Explorer 404 page. But the episode was clearly new as could be: references to later episodes and the series' oft-obnoxious fan community were animated half in full, early-series lazy animation, half with frame-by-frame animation. The episode was later re-re-lost in a site redesign.
Which might have been because of Phil erasing the series from history in the 87th episode.
The Homestar Runner Strong Bad Email series played with this. Sbemail 22 was a missing episode for five months, but not because it had been suppressed or anything; the creators, in the process of creating the emails, had inadvertently skipped over that number. Between emails 40 and 41, they went back and created "sbemail 22" and jokingly promoted it as a missing episode.
Two cartoons, "Marshmallow's Last Stand" and "A Jumping Jack Contest" are absent from the site, but were both released on the "Everything Else, Vol. 2" DVD.
Several Happy Tree Friends episodes have not been uploaded to Mondo Media's YouTube channel. Among them are a "Smoochie" episode with Cuddles, an entire episode of the TV series, one brief Christmas sketch, and two shorts starring Cro-Marmot (one of which is a pastiche of 1930s black and white cartoons, the other being an "interview" with him).