GLaDOS's test of everyone's poker faces has her conclude that all of the characters are abysmal at keeping a straight face. You might think she's being cruel at first, but nope. Playing against them reveals that they have full-body tells on the strengths of their hands.
Sam repeatedly states that he's quite clueless, and why shouldn't he be? You're no longer giving him hints, you're playing against him.
The fact that Claptrap suffers a Logic Bomb from the statement "everything I say is a lie" gets funnier when you realise that the statement ISN'T a Logic Bomb - if it is a lie to say that EVERYTHING you say is a lie, then it stands to reason that only SOME things you say are lies. Claptrap shut down from a logical paradox where there wasn't one!
This also explains GLaDOS' snarky comment afterwards: besides her usual brand of sarcasm, she knew that it wasn't one beforehand. Claptrap being caught by it shows her just how much of a moron he is.
It also results in Wheatley looking smart; while Wheatley was unable to recognize a paradox and just answered it like a yes-or-no question, Claptrap somehow found a paradox where there was none and promptly shut down as a result.
GLaDOS greatly dislikes The Player for being both a mute and responsible in a meta-sense for all of Chell's actions against her.
When Sam starts going into a summary of the events at the end of The Devil's Playhouse and then realizes how ridiculous it sounds out loud, Max pipes in with "I still believe you, Sam." Amusing if taken as a joke; perfectly apt if you remember that Max died at the end, and the Max currently with Sam is from an alternate dimension where they had similar adventures but Sam died.
Similarly, when Sam is mentioning all his time-travel experiences, Max butts in by mentioning how they made a pair of temporal clones. Of course he would say that - he IS one of those clones!
When Sam is the first eliminated in the Borderlands set, Steve doesn't shoot at him, but instead leads Sam away. It first seems like Steve is manhandling Sam, until you realize it's just Sam recoiling by reflex. Sam hates being touched.
Related to this: Why is Sam the only player that Steve eliminates in this way? Because Steve comes from the same game as an enormous, muscle-bound, sociopathic Blood Knight who really loves dogs. Steve does not want word reaching Brick that he fired a rocket launcher at one, as that would end up being very bad for him.
Claptrap states that they represent the four pillars of geekdom: TV, movies, video games, and comics. He forgot the last one: the geeks themselves.
What about the Player themselves?
They are the geek.
Why is Ash so happy about you winning the Necronomicon? Well, not only has he been trying to get rid of it once and for all, but since you're mute, he doesn't have to worry about you reading it out loud and raising the dead.
When the option to buy drinks becomes available, Winslow cheerfully announces that The Inventory has renewed its liquor license (as well as replaced the urinal cakes). Except, if The Inventory is an illegal speakeasy, open in private, why would they need a liquor license in the first place?
Only explanation I can think of is that the Inventory has a legit sister location nearby that they use to purchase bulk supplies(rather than just ordering for...whatever supposed to be blank location they're actually at) and their sister location just renewed its liquor license.
There is a one off joke made by Sam about Max pushing a stick into his eye, before the game cuts to Max, who has, in his own words, “hit braiiiiin…..”. Did Max just accidentally lobotomize himself?!
