The bad thing about the Internet is that, technically, everything on it exists in only one copy. Once the person who's hosting the content stops doing so... it's off to the Internet Archive in vain hope!
Who would've ever thought GeoCities would go down? How many thousands of sites were lost? Granted, most of them sucked, but still!
When Sci-Fi changed its name to SyFy, the URL changed as well. The "Sci-Fi Wire" news website went to its own domain, but lots of old stuff were lost.
Any site, once deleted, is pretty much gone forever. Luckily, the Wayback Machine makes it possible to find at least some of those sites. Among the 150 billion pages saved since 1996, there's got to be a lot of information impossible to find anywhere else, like this fascinating account of an expedition to Kowloon Walled City before its demolition.
Every single internet content made before the Internet Archive.
And before GeoCities, there was Xoom, a popular domain that existed between 1996 and 2001.
The first season of LoadingReadyRun contained some copyright music. However, since it was made prior to the existence of YouTube, the internet was a lot less strict at the time and they were even able to sell DVDs of it. Now they can't even upload most of the videos to their own site. There is, however, one season one DVD being shared around the UK, and there's a list to request it for a week on their forums. The creators ask that nobody copies it or creates a torrent of it, and so far people have upheld that request, making this the only way to view all of the first season. Many of the videos are also available via the aforementioned archival site, but special features and bonus videos are only available through DVD sharing.
The regular and "Hyperspace" paid content on the official Star Wars website. Created in 2003, Hyperspace was the only way to get exclusive — really exclusive — content like video diaries, insider information on the prequels, an unfinished workprint scene from Attack of the Clones, concept art, exclusive commentaries for the original films, and more. However, when the site switched over to a new redesign, all of that content wasn't converted into the site's new Flash format and subsequently vanished into the ether. Short of getting said exclusive content from unofficial fan preservations, there's currently no official way to obtain any of this material. Most of the open content is lost as well. The SW official forums were also closed on June 6, 2011, just after the announcement of the "Complete Saga" Blu-Ray boxset. Given how much information (and interviews with notable Lucasfilm authors and guests) was available on that forum (more than 10 years of it), screenshots of topics and forum posts continue to circulate amongst diehard fans.
While we're on the topic, there have been several official Star Wars documentaries and TV specials that haven't seen the light of day for more than 20 years. They include a documentary directed by Michel Parbot on the making of The Empire Strikes Back (which may have aired on Swedish television in the early 80's), the UK television special Clapperboard: The Empire Strikes Back and From Star Wars to Jedi: The Making of a Saga. While some previously-unreleased older documentaries have been included on the upcoming "Complete Saga" boxset, many of them are still unaccounted for, and can only be obtained through torrents and fan preservations.
Similar to GeoCities, the sudden shut down of iPBFree caused thousands of forums to be lost forever. There was a lot of anger from all parties involved in the following weeks.
The only way anything from image sharing site Fotopic will have survived is if a user saved any images from it for their own worth, otherwise all 8 years of the site history has vanished into the ether after it went into administration. The Wayback Machine is unable to archive anything from it too, and many of the users had their sole copies of their images on the site. It's a pretty big deal.
Any page on This Very Wiki that enters The Permanent Red Link Club or gets an Example Sectionectomy. Even if there were loads of interesting and witty bits, all it takes is one controversial entry and the whole lot goes, never to be saved, never to be seen again. Your only hope is to keep vigil on the forums in hopes of backing up the deleted/castrated pages before they vanish from all records.
The ENTIRE Title Bin was silently deleted. That's a lot of content. All gone forever. How many people approved that?!
Whilst there were some goodreasons for Girlvinyl shutting down Encyclopædia Dramatica and replacing it with Oh Internet, it still represented a MASSIVE loss of recorded internet culture and e-drama. If you could scrape away the Black Comedy you would find a veritable trove of uncensored, documented truth on a variety of matters, pleasant or not. Fortunately several restoration projects sprang up immediately but are somewhat crippled by the fact that the old ED admins aren't going to release the archive, despite not using any of it for OI, resulting in a loss of a LOT of images and text that are hard, if not impossible, to find elsewhere. Some have compared it to burning down the Library of Congress, which, content aside, is a surprisingly accurate analogy.
The First Media Works versions of Bauer Media's Big City Network sites (Key 103, Hallam FM, Viking FM, TFM, Metro-Radio, Rock FM) and Global Radio/GCap Media/Orion Media's radio station sites (Heart/Trent FM/Red Dragon FM etc.), all of which are at http://SHORTENEDSITENAME.fimc.net (example URL). Only First Media Works has the copies, and they're hard to obtain.
As with the Encyclopædia Dramatica article above, it's pretty much the same situation.
Taking it back one stage further, the versions of Bauer Media's Big City network website platform used between August 2001 to May 2005, which was critically acclaimed, and is still popular. Getting a copy is... well, let's just say, not easy.
After YouTube closed down the account of infamous game commentator Kolibiri, his hundreds of videos vanished up completely. Several users have already reuploaded a huge chunk of his videos, but it still seems that a few dozen are still missing.
The first Death Note Abridged by TioH and Dargonakis, made in the days when "abridging community" wasn't a term and LittleKuriboh still had his original account. The concept of this series was mainly the same as the original manga and anime...except that Light was notably...less intelligent, although considering that everybody else was also dumbed down, that really didn't increase his chances of getting caught. It was not only cancelled, but the videos were removed. The only remains are the first twoepisodes uploaded by a fan and a two-part"Best Of" compilation, also made by a fan.
Most of the online featurettes and extra content that promoted Batman Begins and The Dark Knight haven't been released on any official DVD set. This includes TV spots, trailers, making-of videos (which focused on the creation of the clown masks and a retrospective of the first film) from the Comcast website, tie-in television specials (that had exclusive interviews and deleted footage), the "Interactive Batcave" videos to promote the first film from IGN, the first viral marketing clip from The Dark Knight (which had the character Rachel Dawes talking about Harvey Dent at a press conference), and much more.
A video by Doug Walker were he dresses up as Osama Bin Laden.
"Go Cubs Go". A video in which Doug, Rob and Mike get depressed over the Chicago Cubs losing and try to commit suicide, ending with the gun shooting the camera.
A video by That Dude in the Suede that ranted against YouTube's takedowns of The Nostalgia Critic episodes which caught the interest of Doug Walker and in turn was responsible for That Guy with the Glasses/Channel Awesome becoming a showcase for more contributors other than Walker is lost and gone forever. The reason? Suede said he'd delete the video when the dispute between Walker and YouTube had run its course and Suede had saved the video on a now long-gone college computer.
The first version of Neon Genesis Evangelion in 5 seconds. Will deleted it from his channel because he thought it was way too long.
The first version of the first episode of Suede Played, wich was shot in his parents' house, instead of his new one, it also was a normal Let's Play, instead of the second version. It was accidentally uploaded to his YouTube account, and near instantly it was put on private. Thankfully someone mirrored it.
The Spoony One's old film riffs. They were removed from his site in 2008 and he doesn't plan in releasing then again.
His Mashable Awards 2009 Acceptance Video. It was removed from his site and blip.tv hours after it was released due to Fan Dumb calling Scarlet names.
Benzaie's recorded livestreams on his original USTREAM account, wich was closed due to Ben violating Terms of Service.
Every single video made by Daniel "That Aussie Guy" Rizzo for That Guy with the Glasses (except Ask That Aussie Guy and Trailer Trash). While he did upload them to his YouTube account, they are on private mode and his original blip.tv account and his Bored Shitless account were deleted when blip.tv's site got redesigned.
Out of the seven videos that That Chick With The Goggles made for the site, only three were released on her YouTube account and her blip.tv account was deleted.
The second episode of Thanks for the Feedback! (also the first to be shot, supposed to be the last episode and the one who inspired the series), White Rapping, also known by its more popular names, Rape Rap and Rapping About Rape. It was taken down from the site and blip.tv, not because of its nature, because it was the original edit that Lindsay put up on the File Transfer Protocol, told admin not to release it and it ended up on the site due to miscommunication and misunderstanding. It's only available through a mirror.
The Dune, yo video, wich was taken down due to Lindsay iRiff of the film with Noah being intended to replace the review.
After LittleKuriboh's original YouTube account was taken down, there were various videos that he didn't reupload in his CardGamesFTW channel and are only available through mirrors, such as the video were he proposed to his first wife, the video were he dresses up as Kaiba and his four Comment Response Videos.
His LiveJournal account was taken down, taking various posts that were both funny and informative.
Brad Jones of The Cinema Snob has a couple of things you'll never see including:
The Mystery Of The ZenHex is a well known and acclaimed forum that used to allow people to post poetry and other user-created content. The site ended up morphing with myYearbook in 2005, and then banded back off in 2007, losing some of its content. Then, in 2011 the site completely remodeled and all of the site's 10 years worth of content was lost forever. You can view the way the site used to be on the Wayback Machine, but none of the user-created content can be located.
It seems that as of 2012, the site has restored its old database and layout and has restored all non-quiz content to the site... But now is lacking all the material gained between the 2011-2012 newer layout. There's really no winning with this site, is there?
As of 2013 it looks like the forum has officially been retired, and a lot the content can now no longer be accessed.
The change in format caused many games from The N and Nickelodeon sites to go away. You can get a few of them on other sites but most are scams that require you to pay.
Two websites that compiled Japanese game sales, The Shrine of Data (closed in 2005 due to also publishing the American NPD numbers) and Japan Game Charts (closed in 2011) - which even have the problem of not being on archive.org anymore. (It gets worse when you consider The Other Wiki uses both sites a lot as reference...)
Have fun finding old posts on Avidgamers, a server/service that provided the means to make your own community that consisted of a splashpage, a login feature, and then the rest of the site. When Avidgamers went down, it took any content past the splash page with it for every one of these sites.
Any time a M.U.G.E.N site goes down, whether due to a server failure or the owner of the site deciding they don't like their work anymore, a metric ton of stuff usually gets lost. Even worse with WIPs—unless a beta version of the character was released before the deletion, you'll never get to see it in action. The MUGEN community sort of frowns on keeping the tapes circulated, though—mainly due to warehousing, leaked characters and the possibility of people recoding/re-spriting a character and saying it's "theirs".
While this is not the case for most of The Hire, it seems to be the case for the episode "The Follow", supposedly due to contract issues with Forest Whitaker.
Anytime anything gets taken down on YouTube. The video site is notorious for cracking down unnecessarily on users who have videos accused of copyright infringement, regardless of whether or not the videos actually break the law.
"YouTube DJ's" who upload electronic music are infamous for having their channels taken down after 3 years of unfettered activity and millions of collective hits. Greats like HD Trance Music and Maikel631 had hundreds of videos during their heyday, and spawned dozens of copycats, re-upload channels, and name-takers as they were systematically taken down in waves by YouTube and copyright-trolling record labels.
Anime Music Video creators also have it quite rough, as anime publishers and distributors can be quite protective of their work, and a rights dispute over an older series can get AMVs caught in the crossfire. Luckily, YouTube users have a much more "avid" community set up around AMVs, and many have been fought for and won back. Still, it is not uncommon for a creator to give up on reposting their award-winning AMV after getting in hot water, or for an older creator to have abandoned his work.
Neurotically Yours had several shorts and episodes that were lost once the author moved his content to YouTube. Some of the lost shorts or episodes simply could not be shown on YouTube due to the mature content.
YouTube commentator Mskull01 had his channel closed down in February 2013, taking with it his entire "X is not funny" commentary series. So far, it seems that only a very small number of his videos have been reuploaded. He created a new channel at ElyRiffs, but said on it that he would like to move on from the commentary field.
Many YouTube Poop creators have had their channels taken down for copyright infringement, or just closed the channel out of disinterest. Notable examples include Igiulamam, Squirrelous, and CommanderGwonam.
In 2012, a Call of Duty fan hacked the account of legendary YouTube Pooper mark3611 and deleted all of his poops. Fortunately, angered fans have re-uploaded most of his poops.