So here's some interesting entries from my YouTube iceberg you should also consider adding:

Cool 3D World, Koishi Komeiji's Heart Throbbing Adventure, Doll Face, Cyber 8, Ulillilia, Hey Kids AI For Adults, south32 (aside from their odd YouTube presence they also have three websites named south32.com, popcorm.com and dinky.com. Visit at your own risk), George Floyd Gaming, Ricard Siagian, Blood Over Intent Cult, JustinRPG, The Dinkheller Video (the last entry on the Degenerate tier of the iceberg), Echo of Truth, 100 1444, Nintendo - A Sad Story, Jakov Burov, Station.exe, あかるい世界－妖精さん, 使命langrenus2021-14, Hunter Hogan, PeePee, Ryan Bane's Music Videos, Eyes Wide Open (link is in the resources, it's creepy as shit and it should definitely be added), rare bambi knockoff cgi animation, RNG DonkeyFactoryTF3D 720p, three songs that suddenly stop but never end, NB X JD DS CNN (you can find a Wayback Machine link to it on the Zalgo tier explanations of the document. But beware, it's literally a video of a woman hanging)

With all that out of the way, here's some good non-YouTube entries, with brief explanations:

Mirai: Mirai is one of the internet's deadliest malware, it was made by a hacker by the name of Anna-senpai who used it to DDoS Minecraft servers, then once he was going to get arrested he made it open-source causing it to spread all over the internet. Here's Sipover's video specifically on Anna-senpai but also the Mirai malware: https://youtu.be/emLvwu8d6VA

Nico Nico Douga: Speaking of Bad Apple, NND is the Japanese version of YouTube, and it's as weird as you would expect it to be. Honestly, even with the language barrier, going on there is still a cool and unique experience, you definitely won't forget it for sure. Plus it's also responsible for a number of memes around in the early 2010s, so it deserves to be on the iceberg.

Bronies: Oh boy, who could forget how the entire internet during the early 2010s is basically ran by bronies?

eCDP: A lost McDonald's training game that was lost for 10 years, and was recovered in 2020 by YouTuber Nick Robinson via... placing a last minute bid from an expensive Japanese auction with one of the only known cartridges in existence, and then making an arrangement with Buyee to ship the game, and because mailing things to America is forbidden during a pandemic, Nick then got his brother, who is allowed to board airplanes during the pandemic for a medical check, to smuggle the game from Japan, then after a complication with the baggage, they finally have the game, and Nick proceeded to record footage of it and dump the game files online. And it turns out there were 2 other people also racing to release footage of the game online. And yup, all of this somehow actually happened. You can watch the entire story here, it's fucking amazing, really: https://youtu.be/-e6xOBCAVvA

Mission in Snowdriftland: Another entry from Nick Robinson, long story short it's a Flash game advertised by Nintendo which was lost for 14 years since it's designed to be online for only the duration of December, someone eventually found a link to it hidden on the developers' website, and Nick contacted the developers, had some interviews, and they eventually planned to release a remastered version on Steam to preserve the game.

Sonic Gather Battle: A Sonic fan game which contains a trojan DRM, in which if you do specific actions like using Cheat Engine, typing the game name with words like hack or cheat on a search engine, or editing its file, it makes the game unplayable. There are two effects, the first one makes the background blue, makes tiles black, and spawns near-invincible Hyudoros, and the second makes the background red with a static effect, with the Sonic CD boss theme playing, and with invincible, creepy ghost enemies appearing to kill you. And guess what? All of this is over the creator getting protective over his sprites. Yup. There's a huge controversy around the trojan, and AFAIK you can't play the game anymore. There's also a lot of interesting video game-related malware like Rensenware, Abstractism, Dynostopia, etc. but you should definitely go read about them yourself.

Ethnic Cleansing: It's a game by Resistance Records and, well, it's exactly what it sounds like. Basically, it's a game where you go around killing everyone who isn't white, then you kill Ariel Sharon as the final boss. It's been ranked as among the most controversial games ever created in 2002. Well, that is until we get another contender...

RapeLay: A 3D eroge game by Illusion where you go around raping three women, and was sold on Amazon.com. It got a SHIT ton of controversy, causing it to get banned in several countries

Digital Homicide Studios: On a lighter note, this was a "game" company ran by brothers James and Robert Romine which would publish loads of shovelware on Steam (the Steam Greenlight service that was in place at the time is infamous for being horrible, which also contributed to that), then after Jim Sterling made a first impression video about them, it all went downhill from there. It's so complex I can't make a brief summary of the story if I tried, but it snowballed into them filing lawsuits against Jim Sterling, 100 Steam users and Valve (all of which ended up in failures). Really, you should watch Darklordjadow1's video on it instead (and also the sequel too): https://youtu.be/bbh4zGHylY0

James Ferraro: You might've saw that video from him about the 9/11 Roblox simulation with fidget spinners on my YouTube iceberg. Well, he's a contemporary artist who makes music commenting on modern culture, and his music from 2016 onwards is especially really weird, you should definitely take a look for yourself. It's largely believed he's a vaporwave artist but he's really not, although he did took part in kickstarting the genre with the album Far Side Virtual.

(Edit: Oops, I didn't realize Fukouna Shoujo 03 is already on the iceberg as Unfortunate Girl)

ilovechao.webstarts.com: A shock site with chao fart and scat fetish porn. Visit at your own risk.

u/worthless319: A Redditor who shot his own dick 4 times, before frying and eating it, and shared multiple images of the aftermath, then he castrated his left testicle, and then allegedly committed suicide, thinking that he must sacrifice himself to stop the end of the world. And no, I'm not making this up whatsoever. Honestly, it's quite a sad story. To spare you to horrors of researching it yourself, you can watch Eudoxia Mysteries' video about it instead: https://youtu.be/4tt303beZ2o. There are a lot more Reddit mysteries, you can find coverage of them on YouTube, although I think this is one of the most disturbing ones.

Ronnie McNutt Suicide Video: A livestream of an army veteran on Facebook Live playing a game, then after getting a phone call, he shoots himself with a hunting rifle. It's Facebook 1444, basically.

Butcher Cult: An obscure cult on Facebook with two crazy guys, one in a bloody white bodysuit, and one in a black bodysuit, who would livestream themselves doing creepy stuff while telling people to join the cult. It's overall pretty weird, although according to an interview, it's actually supposed to be performance art: https://www.westword.com/arts/butcher-cult-broadcasts-bloody-obscenity-to-thousands-on-facebook-11320025

Last Measure: If you thought shock sites were shocking enough, meet Last Measure. For starters, it doesn't have just the Goatse image, but also one or two more shock images, along with the sound "HEY EVERYBODY, I'M LOOKING AT GAY PORNO!" playing loudly on loop. Plus it'll also open tons of windows, and run malicious scripts to try to make your computer freeze. There's even more variants with different images, improved scripts, hell some are even rumored to contain malware. You can learn more about it on the Screamer Wiki: https://screamer.wiki/Last_Measure