This is a very common phenomenon on YouTube, due to their often draconian policies regarding copyright and localization, as well as their clunky maintenance of content (unsurprising given the sheer, overwhelming volume of videos that they host). Full series playlists are almost always a crapshoot, especially if it's a Long Runner (such as The Angry Video Game Nerd), and especially if it's fan-made. For the most part, you're better off referring to the creator's website if you want access to a gapless catalog.
Several early lonelygirl15 videos have been removed from the official listing (in some cases, probably due to copyright infringement); namely, "First Blog / Dorkiness Prevails", "School Work in Summer... BLECHH!!!", "Grillz feat. Danielbeast, LG15, P. Monkey and O'n.", "Proving Science Wrong", "My Lazy Eye (and P. Monkey gets Funky!)", "The Tolstoy Principle (and Dad "talks" to Daniel)" and "Daniel, Be Careful". The videos are referenced on numerous occasions in later episodes and still viewable on YouTube.
The later series 1 episode "Uncle Dan (D-Bone Remix)" is missing from both lg15.com and YouTube, but is viewable on Revver.
Thanks to Yahoo shuttering GeoCities in 2009, it is now gone again from the web.
Most of the first season of LoadingReadyRun is unavailable; in the early days, videos would be phased out to make room for newer ones (this was before the existence of YouTube). Most of the episodes have not been reposted, due to some of them having copyrighted music, the crew being busy with other things, and that most of them were just plain bad.
The success of Marble Hornetsled to the creation of dozens of parodies and original vlogs, many of which were subsequently abandoned (for a variety of reasons) and removed. A list of dead/inactive series can be found here and here.
Limyaael's first Faean novels, the Orlath trilogy, were taken down from Fiction Press due to someone plagiarizing them (Or something). Which is a real shame, because what little is known about the plot of those novels, both through Limyaael's comments and the other novels taking place in the same universe, seem to indicate that the trilogy was an absolutely brilliantDeconstructive Parody of cliched fantasy.
Draw Your Own Story episode 1-9 and a good chunk of episode 10, due in part to moderators deleting old threads on the forum where they were hosted, and in part due to the site being hacked and a lot of uploaded files (i.e. images that made up episode 10) ending up lost forever. What little we know of them is pieced together from memories as well as old episodes still on the contributors' hard drives.
Several writers of the originalDarwin's Soldiers RP on Furtopia played out scenes via private messaging. Those scenes were never released.
An early website for Back to the Future: The Ride featured a tour of Doc Brown's institute. One page contained some clever blueprints of Doc's post-trilogy inventions, including a personal time travel suit, a hover-bike, and an improved Mr. Fusion. Sadly, the Internet Archive only saved two captures of the blueprints section, and neither one successfully captured all of the blueprints.
The Viral Marketing sites for District 9note including D-9.com (where visitors could view a satellite map of District 9 and receive "news alerts" of suspicious non-human activity), an extensive MNU corporate website, and a Prawn activist blog run by Christopher Johnson have been lost completely. The unofficial wiki captured a few screenshots and preserved some of the information in text form, but anything added to the sites after 2008 was lost.
The website PO.B.R.E. is dedicated to archiving translation and romhacks in Brazillian Portuguese. Unfortunately, the are a few missing translations.
Pornographic pay websites often have some videos that simply vanish after a while. Reasons vary, from the video being unpopular to unforeseen legal troubles to the girl turning out to be underage, but one rather heartwarming example is the "Sandra" episode from the famous Bangbus site. The reason Sandra's video disappeared from the site? She and the webmaster got married!
The Cinema Snob episode on Grizzly II. The movie itself was unfinished and thus never commercially released. The film's producer found the review and ordered it taken down. Since Fair Use laws become extra muddy with unreleased material, Brad complied and took it down. (Although his review can be found on youtube.)
Brows Held High episode on The Girlfriend Experience was made before Oancitizen joined TGWTG, and it was reposted on the site when he was too busy to make new episodes. Problem was, that on the initial run, the show was known by few people, and most of them friends, so no one pointed out the sexist undertones in many jokes. On the site, several fans got angry, which led to Oancitizen removing the video from his account, and recording a commentary apologizing for it. And the less we say about Shit TGWTG Fans Say, the better...
And now his episode on Crispin Glover's What Is It? is gone. Though for reasons similar to the Cinema Snob example above, the movie has no commercial release and is only allowed to be played at private screenings with Glover's presence.
Jack Douglass of Jacks Films included a "Tool of the Week" segment (in which he criticized and mocked a fellow YouTuber) in an early installment of his Featured Fridays videos. Viewers complained about the uncharacteristically mean-spirited tone of the segment, and Jack removed the video several days later with an apology, admitting that he was just trying to be "edgy".
Although listing all the cities would take up several pages, Google Street View's coverage of England 2008-2009 for cities in the United Kingdom have disappeared, leaving us with only 2012 pictures of places like Salford, Middleton etc. and not the Unintentional Period Piece ones from 2008-2009 - which are themselves an important primary source for historians and students.
Some posts from Hyperbole And A Half have been removed. Allie, the creator, explained this is is either because they contained information that might make real people in the stories uncomfortable or just because she finds them embarrassingly bad.
The San Francisco 49ers' video was taken down after two players, in the heat of the controversy surrounding Chris Culliver's homophobic remarks, denied ever making the video, and when reminded of its existence, said they did it under false pretenses.
Oscar Pistorius' video was taken down after he was charged with murdering his girlfriend.
A re-upload of the Dr. Mario Song from brentalfoss, removed after 11 months due to complaints in Feb, 2013. The file is still in Homestar SB 9 (aka LOL it on here)'s computer.
All of the Adventures of Slinky videos from I Am Bagel, due to the fact that they weren't scripted. The only trace of it left is on this video and the CN/Hub/Nicktoons on YouTube block on the livestream channel. There was a article of it on Nick Fanon but it brings up a deleted article.
As of November 8, 2014, the whole Slinky series has been deleted with the entire "CN Hub Nicktoons on YouTube" block being removed completely for a major rebrand of the Live Stream channel and the video being deleted, making the whole series lost.
All of Matt Boo's videos were removed by May 2014 due to many videos being deleted from CN Hub Nicktoons by an unknown offender, driving him to quit and remove all remaining videos he did so he could move to his own channel. Only three select videos still live, albeit on Matt Boo's new channel, two of which are unlisted and are only accessible by an announcement video. Some other videos survive on his PC but he has no plans to upload them.
On May 2013, when Flipnote Hatena was ending, Matt Boo uploaded many of his flipnotes to CN Hub Nicktoons. When the videos were removed by an anonymous user as mentioned above, the flipnotes were included. The only way to access them is on Sudomemo (well, some of them, anyways).
The Mario Party TV players have made mention of 'lost episodes', gameplays that for one reason or another was either not uploaded onto the channel or not recorded altogether. One noted one was a run on Mario Party 7's Grand Canal sometime before the playthrough for the Summer Salt season, one where (yet again) Mr. Doom had an insanely good amount of luck. Clips from that episode were used as The Stinger for the 'canon' playthrough.
Mr. Doom ended up finding a lost episode (a playthrough of 6's Castaway Bay) when he was going through his hard drive and posted it on his personal account.
One of the threads that the work known as Update consists of was deleted from the forum it's hosted on, but still exists in a PDF archive being circulated and downloadable.
Achievement Hunter's Let's Play of the Magic: The Gathering Xbox Live arcade game was apparently filmed, but not uploaded. Any reference they make to it implies that it was incredibly boring.
There's also an episode of Let's Build that has been removed due to Internet Backlash from finding out of a game Geoff and Gavin played that many people realized tantamount to stalking. Both realized that, indeed, it did and apologized profusely over it.
Prominent SCP Foundation writer Fishmonger had a falling out with the site and demanded his works be deleted under threat of legal action. His SC Ps and other works are lost.
They're not really lost, since an archive of (most) of his works can be found here. However, they can't be found on the SCP-wiki anymore. The others that are not included with the zip really are lost though.
Many YouTube Poop creators have been hit with this over the years, usually due to the poop getting taken down because of a copyright claim.
The Nostalgia Critic was going to have a tribute video dedicated to Rachel, who left the show as of the Face/Off review. As mentioned in the actual episode, this video was accidentally deleted.
ClickHole originally had a video called, "If You Grew Up With 'Calvin and Hobbes,' You Need To Watch This Right Now". It was aRule 34video. The video was soon removed, and trying to view it through the site's URL redirects you to the YouTube page of the removed video.
slowbeef and Diabetus had a test run of a Retsupurae livestream, but never bothered to save the video of it. Thankfully, one person watching actually did save the recording and it was later put up.