Their Shitstorm 4: Matt and Pat's Scariness Marathon special series of videos is so called because of sort of a goof from Matt. During one episode of their Superbestfriendcast in which they were talking to Guy Cihi, Matt brought Shitstorm into the conversation but hesitated on swearing in front of their guest, so instead referred to it as "Matt and Pat's Scariness Marathon" in an awkward manner. After the interview the other guys ribbed him about it, and the rest is history.
The original upload of the Saints Row IV video on Machinima was uploaded a few weeks prior to the release of the game (the Best Friends had received an advanced review copy for the show), but was removed about a day after being uploaded. The video returned weeks later when the game came out, but with a very noticeable edit at the end to anyone who saw the original upload. The change to the video's ending in the re-upload version seems to indicate the reason for the original video being removed was due to the inclusion of a pretty major spoiler, especially with the game still weeks from being released. For those curious, the original video ended with Zinyak destroying the planet Earth at the end of the game's third mission.
Before the game even starts, when Woolie says that Ellen Page and Willem Dafoe are the only ones that can potentially save this game, Pat quips, "Yeah, you love those hamburger phones that go crazy and crossdress!"
Blooper: The initial upload of the The Punisher (Capcom) video had a scene where Matt paused the game to answer a deliveryman at his door, and could be heard speaking French to said deliveryman (meanwhile Liam asked "is it for me?"). The inclusion of this blooper went unnoticed by Matt at first, but a few days later the video was suddenly altered to have this editing blooper removed from it.
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.
Invoked with their playthrough of D4, in which one of the explicit goals is to encourage more sales of the game so that future chapters can be made.
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.
He Also Did: Years before Two Best Friends Play, Matt made the "Street Fighter Stupidity" video compilations among other stupidity compilations, he also had his Final Fight deviantart used as cover by a few other people.
I Knew It!: Happens a lot during their Beyond: Two Souls playthrough, since they are so Genre Savvy (and the plot rips off so many cliches), that 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 stillborn 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!
Trolling Creator: Their BlazBlue video possibly being their best example but their attitude toward comments criticizing their gameplay or pronounciation is pretty much making it worse.
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.
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 Let's 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 Let's Plays still occur, but NSMBU will likely continue to stay a standalone video).
A video for Daylight was recorded for one of the Shitstorms, but it was never uploaded because Matt and Pat felt the game was so boring that they couldn't get any interesting commentary out of it.
They had a hide under coats as a parody of survival tips video and one of their Running Gag. They had too much trouble and considered it wasn't good enough.
A full Persona 5 LP was planned, and even announced on the podcast. It was promptly cancelled less than a day later after Atlus released restrictions on spoilers so severe that it would essentially make it impossible to do a full LP.