Liquid: You, the anti-hero who crosses the line of morality so frequently and with such audacity, that it brings out the cheepest of laughs.
Art Shift: Episode 7 is done in silent film style, due to technical difficulties on LordQuadros's part.
Or because it made a handy in-universe excuse to do a silent film episode that had been planned beforehand.
Author Filibuster: The finale has Liquid and Snake debating abridging ethics. An odd case in that, while both sides have flaws in their arguments, neither side is entirely wrong, either.
A Wizard Did It: Whenever Snake asks for explanations to certain illogicalities (such as how he can use the Codec without being heard, or how his informant knows his exact location), he just gets the answer "Magic!".
Hand Wave: The less you know why the terrorist want Big Boss's remains, the better.
I'm a Humanitarian: Snake decides that leaving a large, perfectly good body is a waste (and expresses relief that he can give up rations) and at one point expresses a strong desire to eat Sniper Wolf for revenge.
Raiden: Again, these are things that everybody in the world knows...But go on...
Bait and Switch: Episode 0 starts with the intro speech to Snake Eater instead of Snake's MGS2 intro, but starts up normally afterward.
In the series proper, Raiden attempts a Snake impersonation during the beginning of Episode 1, but Campbell tells him to "Knock that shit off".
Better than a Bare Bulb: A lot of times. Vamp in particular moves on from making innuendos to being this, with regards to his role in the series.
Blatant Lies: Campbell's instant denial of any other intruders being in the base even though Raiden just saw him.
Boss Banter: Deconstructed. Solidus keeps taunting Raiden from within the Harrier, but it distracts and annoys Vamp, who is trying to pilot.
Call Forward: In regards to the source material, at least. In the finale, Solidus begins a sinister speech, but gets interrupted by Raiden, who is using the exact same words the original Raiden would later use against the Final Boss in Metal Gear Rising: Revengeance. Complete with raspier tone.
A short video released at the beginning of 2014 using footage from the same playthrough has Otacon, Snake and Raiden predicting the future. Otacon and Snake start thinking about Metal Gear Solid 4: Guns of the Patriots (because it's set in 2014) while Raiden headbangs to "Rules of Nature" from Revengeance. The other two give him weird looks.
The Cameo: Paul Eiding as "Big Teddy" in the opening of Episode 9. Very much an Actor Allusion, given the part of the game that episode covers.
Character Filibuster: The Colonel AI (with help from the simulated Rosemary) goes on a four minute-long speech about how the failure of DMCA means nothing given that SOPA has been proposed, the Patriots' ultimate ambition to monetize abridging and parodying as advertisements for the source material, and how Raiden (and all the stale jokes in this series) has played perfectly into their hands, concluding that Raiden forms a perfect Audience Surrogate by being amused at such stale humour, covering both This Loser Is You and Take That, Audience!. This is very much in keeping with the original MGS2, where the Patriots rant at length about societal control.
Solid Snake has a particularly heartwarming one after the end credits roll, about how one really shouldn't care about corporatism or being hated when making original work, and that as long as you're proud of what you've done it's worth it in the end.
Compressed Adaptation: it is an abridged series, after all. Still, it can be startling to see the entire Tanker half of the game squozen into exactly 481 seconds.
Large Ham: Most hamminess is rather subdued, but Solidus makes up for it. Even in-universe, he strives to be as dramatic as possible at all times.
Mind Screw: It's Metal Gear Solid 2, a competitor for Mind-Screwiest video game out there. Of course this gets lampshaded repeatedly, to the point of the opening theme being Everything You Know Is Wrong.
The Scream: Raiden's reaction to being told he has to talk to Rose.
Sequel Hook: To the inevitable abridged series of Metal Gear Solid 3: Snake Eater. Quadros himself talks to Snake and tells him that he can use a file on Emma's disc. That file has information on Operation Snake Eater.
Shown Their Work: "McPhayckneighm" states that although Shell 2 exploded, the hostages were fine because since it was Sunday, they were all in Shell 1. Raiden contests that it's actually Wednesday. April 29th, 2009 was a Wednesday.
Take That, Audience!: The Colonel AI's rant on how only the throwaway jokes were considered funny and that nobody appreciates creativity in this information age. Lampshade Hanging when he bets that people are about to down-vote the video and unsubscribe from the channel.