In the beginning of their Walking Dead playthrough, Matt assumes that Lee was innocent of his accused crime, instead believing it to be committed by "the one-armed man". Given how Lee did commit the crime and loses his arm later in the game, he was technically right.
Pat: (While viewing a Loading Screen with Snape on it) Guys, you gotta do potions or else Nakatomi Plaza will go up in flames!
Colbert Bump: T.E.C. 3001 has gotten a fair bit of publicity thanks to their ringing endorsement of the game in the second Xbox Live Indie Games video, prompting the developers to publicly thank them.
Creator Backlash: Downplayed. After 11 episodes, they decided to end the Mailbag segments indefinitely, not out of anger (they make it clear throughout the episodes that they adore their fans), but because they had become so overwhelmed with gifts that they were running out of room in their homes.
Fake Nationality: Slowly averted as time went on. The guys initially passed themselves off as American, but over time they revealed their real, Canadian nationality.
I Knew It: Happens a lot during their Beyond: Two Souls playthrough as more and more of their predictions about the plot come true. The biggest of these, however, comes right at the end from Woolie, for guessing that Aiden was really Jodie's unborn twin brother less than halfway through the game.
Also happens a lot in The Walking Dead, though largely due to being genre savvy.
Old Shame: Fighterpedia. A series that lasted one season before Two Best Friends properly took off featuring Matt and Woolie discussing the intricacies of fighting games. To sum up Matt's feelings about it:
Woolie:*picking his character* Representin' that 'Pedia!
Matt:*laughing* No one cares about Fighterpedia, not even me!
*cue title footage of Fighterpedia mentioning how much it sucked*
The Shitstorm of Scariness 2 video on The X-Files: Resist or Serve got removed from YouTube after a copyright claim from FOX got it content ID'd. Thankfully the launch of the new Super Best Friends website, which doesn't have to deal with YouTube's finicky content ID system, now has the video up and viewable for all here.
Pat: It came out! Matt: No... Pat: It came out! Matt: Okay, you encoded something on a disc, and you put it in here to troll me. ... Pat: Downloadable content?! They still didn't finish the whole game!
Vitriolic Best Buds: Although they're good friends now, it is revealed in a interview that the two strongly disliked each other when they first met.
What Could Have Been: When Matt came up with the idea for the original video, Two Best Friends Play Kirby's Epic Yarn, he wanted it to be himself and Woolie. Woolie thought the idea was stupid, and declined to take part. Pat was Matt's second pick, even though they weren't even very good friends at the time.
Woolie has gone on record saying the reason he turned it down was because he was busy watching Street Fighter IV streams when asked, and at the time didn't think the idea was worth spending his time on. Nowadays he jokes that he semi-regrets that decision.
Apparently, there was going to be a Bioshock Infinite episode, but due to the controversial content, they found it difficult to approach without sounding insensitive.
There was a "Super Best Friends Watch" of Metal Gear Solid 4, and it even had some episodes made, but they were forced to drop it when Konami threatened to sue.
An Asura's Wrath Let's Watch was stopped as well.
As Pat revealed on Retsu Talk, they were gonna do a Peace Walker lets play, but unfortunately Konami threatened to sue yet again.
New Super Mario Bros. U was planned to be a series, but the first video had the unfortunate timing of being uploaded around the same time that Nintendo was removing monitization from Lets Plays in May of 2013. Nintendo's stance on LP monitization was reversed just a month later, but by that time the guys had already moved on to a busy schedule of doing other games, so they opted to not continue the series past part 1 (Nintendorelated Lets Plays still occur, but NSMBU will likely continue to stay a standalone video).