Internet Graveyard
- "If it's on the Internet it's there forever" they said
Geocities
1996-2009
Yahoo killed it. It had 38 million pages and was still one of the top 200 visited sites.
"In 2009, Yahoo! succeeded in destroying the most amount of history in the shortest amount of time, certainly on purpose, in known memory. Millions of files, user accounts, all gone." - ArchiveTeam
Sure, most of those pages were crap. Yet...
A huge number of primary sources (mostly between 1996-2003), the Internet vernacular written by mothers, fathers, gamers, new-age hippies, gays/lesbian/trans, conspiracy theorists, Neo-confederates, etc, got steamrolled out of existence, replaced by... a mention in some Internet articles? Nothing at all?
Even though much of GeoCities ended up being archived, I doubt there are many people looking at it today. Now that it's all been swept out of sight, the history of the Web can be written to look something like this - how a few startups made the web "safe" for normal people, and made a lot of money in the process. Yeah, something like that.
(Ironically, these GeoCities "web pioneers" were considered part of the eternal September by an earlier generation of Internet users. After all, how hard is it really to sign up with a free host and bash together some HTML tags?)
- Google Videos
2005-2012
Google never bothered to save it after buying YouTube 
Dissolute Productions
2005-2012
small flash site
Metroid Headquarters
2004-2013
Metroid fansite- Viddler
2005-2014
Competed against YouTube; lost - Blip.tv
2005-2015
Many Internet creators posted here to avoid YouTube's restrictions - The Kid From Brooklyn
2003-2016
Opinionated New Yorker with a projecting voice, passed away in 2013 - Screwattack
2006-2016
AVGN and other retro games YouTubers used to post here - NeoDelight
2002-2016
Flash game site, appears to have been bought at some point 
DeletionQuality
2005-2017
small flash site- Comic Dish
2006-2017
A web comic host that shut down. Several comics have no surviving archive. Were they any good? We'll never know. - Quantum Ascension
2014-2018
A sci-fi setting seemingly inspired by Halo, then later abandoned 
Customize.org
1998-2018
popular site for skinning Windows XP back in the day- FunOrb
2008-2018
Java games made by Jagex, better known as the RuneScape company. - Duo Radon
2004-2018
Just one example of a furry artist website, nsfw if you can get any pictures to load. - Tinypic
2004-2019
millions of dead forum links - The Spoony Experiment
2004-2019
check the Internet archive for his old videos * - NintendoAge
2008-2019
A site with a lot of Nintendo content, which had all of it's features deleted after it was purchased.
Although I wasn't personally involved in the site, it's death seemed noteworthy enough to include here.
NintendoAge used to feature it's own used games market and ezine series with some unique interviews from people in the game industry.
In 2019 the site was bought by a comic-collecting-as-an-investment company called GoCollect, which deleted the games database, forums, and every other feature of the site. The deletion was so total that I don't count this as a "technically not dead" site, even though the domain is still in use.
The ShyGuy Kingdom
2002-2020
A site dedicated to the collection of game sprites - including a few customs that were never uploaded to The Spriters Resource.
Macromedia Flash / Adobe Flash
1996-2020
Once a ubiquitous web format.
There is something about the death of Flash that strikes me as odd - it wasn't allowed to simply be phased out, companies went out of their way to murder it, with browsers blocking it's use entirely, and Adobe not providing downloads even for legacy purposes. The whole industry joined together with the singular purpose to kill a feature of the web.
How many of it's faults have simply been replicated in the javascript-heavy websites of today? Excessive consumption of battery? Security vulnerabilities? Though I will concede to those who critisized Flash on the grounds of it being a closed system owned by Adobe.
And a moment of silence for all the deleted Tumblr blogs, important to someone and now gone
- Sites that technically aren't dead.
- B&A Products On-Line Catalog
1997-2012
I'm not sure what catastrophic future these maps were supposed to represent, but I'm disappointed they're not for sale anymore. - Imageshack
2003-2016
Another mass-image deletion. - Photobucket
2003-2017
Pulled the plug on free hosting, killing millions of forum links and charging a ransom of 400$/year. - Flickr
2004-2019
Cut the upload limit for free accounts, deleting old photos. - Cinemassacre
2003-2020
Though the site still exists, evidence of James' pre-AVGN films and old blog posts have been removed. What remains is essentially a YouTube mirror.
James Rolfe had made hundreds of short films before AVGN. The original purpose of Cinemassacre was to showcase his filmography to a wider audience. Something that wasn't possible in the days of passing VHS tapes around.
I won't get into the controversial "why", but in 2020 the site was redesigned into a social media link dump.
In 2021 the site changed again, now showcasing videos like it used to. However, evidence of his original filmmaking passion and his old blog posts have been removed.
What remains is a one-to-one YouTube mirror.
- Miniclip
2001-2022
Old games were removed to rebrand as a mobile game developer.
How many of your favorites on YouTube are missing?
- Other websites about the death of websites
- Deathwatch How could I beat this? A compilation of thousands of websites that have died or are expected to die.
- Web Design Museum Screenshots of many old websites, focusing on ones that had interesting designs.
- Killed by Google The quintessential list of projects killed by Google.
- Embrace Creation - An Archive An archive of abandoned Pokemon fansites.
- Cyber Mauseoleums Not all websites are abandoned by choice.
- The Memory Lane Mausoleum
- Dead Game News Semi-active series about the shutdown of online games.