Critical Research Failure: When talking about Sonic.exe's origins in his "CREEPY SONIC GAMES" video, Jeff mentions that it originated as a trollpasta (complete with showing its article on the Trollpasta Wiki). Little did he know that it originated as a serious Creepypasta but it ended up thrown away into the aforementioned Wiki due to negative receptions (and a bad case of Can't Take Criticism from the author).
Hilarious in Hindsight: In Super Smash Bros. Mods & Glitches, Jeff jokes about Steve "not showing up to the next Smash predictions video". Two years after the video came out, Steve himself (along with Alex, a Zombie, and an Enderman) would eventually be announced for Super Smash Bros. Ultimate.
LUIGI Fan-Games! includes a segment on Super Luigi Country, which opens with an amusing MS Paint cinematic, but when the game starts with reused assets, Hammy reacts as if it's a huge step down. Though the game is rough, throughout the segment the graphics are shown to be competently implemented compared to many of the other games featured, making it unclear what the problem is.
There's a similar moment in Weird Legend of Zelda Fan-Games! where he quits after reading a single line of dialogue from Darkness Uprising. The graphics appear fine, and the story doesn't have time to show off anything strange, so it comes off like the punchline is missing.
The games he covers in Creepy Mario Games, such as one that features what looks like a normal Super Mario World game until a new level opens up called "OH GOD NO", featuring long hallways, blood coated enemies, and a horrifying fight against Luigi.
The Barney games video. The Barney doll he talks to in the video makes his first appearance with Offscreen Teleportation, and it just seems to stare at Jeff throughout the entire video. The game footage has several red-tinted closeups of Barney's facial expressions, he crushes a bear to death, and generally seems like a creepy stalker in a purple dinosaur costume.
The video on creepy Sonic the Hedgehog fan games (and Sonic Dreams Collection), natch. Clips from the games themselves count, especially from Help Me, which includes a nasty montage of creepy images and sounds.
And then, there is his second Creepy Mario Games video. Bar the annoying jumpscares and frankly slapdash quality of all the games, the general setup for the episode dives headfirst into Surreal Horror. The final game he plays is the infamous Super Mario World ROM hack, 'the. The game is freaky enough on its own, but then he had to go and add voiceovers to the random strings of text in the hack. They're so genuinely unsettling that you'd think they were actually part of the game, until you see a more normal Let's Play (or play it yourself) and notice...nothing.
Overshadowed by Controversy: The comments on "Dragon Ball Fighter Z MODS & GLITCHES!" talk less about the hilarity of the video's subject and more about the sponsor whose problems Jeff (apparently) did not know about. (Look up "The Art Institute scandal/scam", and you will see)