Any fanwork in a fandom under a Fanwork Ban usually becomes this. As most sites are pulled for fear of invoking legal wrath, some fanworks are made available through shady underground communities.
The Star Trek fanfic "A Fragment out of Time" by Diane Marchant — the first Kirk / Spock fic ever written, and the story that spawned Slash Fic as a genre — exists today only in its original zine, Grup 3, which is extremely rare. The story was never posted online. The only way to read it is to hunt down the zine in used bins at conventions. The University of Iowa Library, however, hosts a special collection of early fanzines, including Grup 3 and the zine that contained Marchant's defense of K/S — Grup 4.
This is actually true of many of the early fic written in zines, as many authors never made the switch to the Internet.
Computer Boy, an Australian parody of The Matrix. No DVD release and only available as a low-resolution Quicktime download, due to (apparent) legal issues with a scene filmed inside a McDonald's store.
It has been known for fanfic authors who turn pro to pull their fanfic from the internet, either because they consider it Old Shame, because their publishers don't approve, or because they're strip-mining their fic for ideas for original works and don't want people to make comparisons.
It's not just ones from authors that turn pro. Any fanfic can just disappear from the internet due to some reason from the fanfic author. Sure, most of those aren't worth reading, but there are some good ones that disappear too.
Snow Angels is only notable because it has a works page, but the author has long since pulled it from FanFiction.Net. A Dramatic Reading of the first few chapters does exist on YouTube, but the videos have been made private (so only the dramatic reader's friends can see them) after somebody the dramatic reader knows in real life mistook him for the actual creator. Since Snow Angels is So Bad, It's Good...
When an Internet domain goes under, works by inattentive authors using that domain will disappear. The end of Geocities killed quite a few fanfics on unmaintained sites which had been popular enough to stay up by reader visits alone. Ones on Tripod and Fortune City have also disappeared.
Anything that was on Soupfiction and is not in the Wayback Archive.
Kelly Green seems to consider her earliest, adulated Haunted Mansion comics terrible and deleted them for DeviantArt. Emma Mosier also deleted some of her early Phantom Manor doodles after being harassed by shippers who shamed her for her "Phantom/Melanie" AU. Fortunately, through a combination of fans having made personal copies on their hard drives and the ever-useful Internet Archive, most of those comics have been relocated and copies can be seen on the wiki.
There used to be Touhou fancomic by pixiv user Wimifu, the which has a child Ran being raised by Yukari but, for some reason, the artist took their pixiv page down (or hid it, as the Wayback Machine says it's still around), thus the only way to view a good much of the comic and the artist's other artwork is through imageboard sites.
Kill la Kill fanartist "Herokick", much like the above example, hid their tumblr page and left their AU comic uncompleted, thus the only way to view much of said comic (along with other fanart) is on their twitter page and imageboard sites.
Fan-videos of any kind (AMVs, Abridged Series, "crack" videos, etc) when the user account is either A), taken down, B), terminated by the site, and or C), the videos are muted/blocked from viewing (more often than not in the case of YouTube). Fortunately, if fans are diligent enough, there are usually mirrors.