The TVTome Adventures movie is gone. The site which originally hosted the entire series 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.
Production images of a Deadpool animated web short. The animation was cancelled and remains unfinished.
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.
The unedited Strong Bad Email #69, "personal favorites", lacks an archived copy.
A Howard the Duck animated short was available on Marvel's website, but no archived copies have surfaced.
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).
One episode of Neurotically Yours has Foamy going on a rant over the current state of Halloween. At the end of the episode, Germaine gets electrocuted by a monkey, causing her breasts to swell up until they explode in blood and gore. Some time later, the breast explosion scene was cut out.
The Barbie: Life in the Dreamhouse episode "New Girl in Town", which introduced Black and Nerdy Grace, was marked Unlisted on Barbie's YouTube channel for a few months. The Life in the Dreamhouse Wiki attributes "bad comments" as the cause. Grace's next episode, "Malibu's Empirical Emporium", didn't even receive an English release, until April 2015 — four months after Mattel shared and took away some dubbed versions of it.
In 2002, Sony Entertainment optioned Lenore the Cute Little Dead Girl for a possible animated movie release, but they couldn't come to artistic terms with creator Roman Dirge, so eventually they let the rights go back to him. In the interim, however, they produced a series of twenty-six Flash animated shorts based on the Lenore comics and hosted them on their Screenblast service. They took them down around 2008 or so, and have so far refused to release or re-host them, with fansites or YouTube as the only place to see them.