In second to last mission of the first Splinter Cell, when you blow up a truck with unassembled nuclear weapon components inside two guards outside will be alarmed and will run to the source of explosion. Suddenly one of them stumbles and comically falls flat on his face before getting up.
Michael Ironside did a interview on Double Agent and had a couple of funny lines.
I was on a plane going to London, and I asked for a coffee. And I heard someone go Sam Fisher, and I'm going, what? And I look up and there's this guy in an undone three piece suit going, You're Sam Fisher, and I went, No, I'm...I'm, wait a second I guess I am.
Sam Fisher could have been very two dimensional. He could have been very flat, cardboard, finish him...squiiick.
How about this conversation from Sam's Navy SEAL days?
Vic: My kids never draw me pictures or write or anything.
SEAL: They don't write 'cause you can't read, man.
Vic: Laugh it up. But when I get out of here-
Sam: You're going to kindergarten?
SEAL: You know I hear that they've got entrance exams in kindergarten now, Sam... I dunno if Vic's gonna make it in.
Sam needs someone (the vice president of the United States) to stay where they are without killing them in Conviction. ("SECURE") How does he do it? He nonchalantly blasts both of his kneecaps with his pistol, of course.
DPRK Soldier #1: You said there were eight crates in the delivery, but I only see seven.
DPRK Soldier #2: What you do you mean 'seven'?
DPRK Soldier #1: As in one less than eight.
DPRK Soldier #2: Well, the bill of lading said there were eight.
DPRK Soldier #1: Did you count?
DPRK Soldier #2: Uh, well...not exactly...
DPRK Soldier #1: Not exactly? It's just not that hard to count eight giant crates!
In Blacklist, the Action Prologue shows Charlie and Sam talking after a very serious situation. When Sam brings up Sarah, Charlie asks if she's still single. Sam's reaction is a Death Glare that shuts him up. Overprotective Dad at its finest.
Kobin. Even after saving Fourth Echelon's asses twice and helping them with black market intel in Blacklist he still gets locked up in a cell aboard Paladin.
In Blacklist's second Briggs co-op mission, Sam and Briggs capture two suspects. While Sam is interrogating his, Briggs' manages to free himself and snatch his gun, now holding Briggs at gunpoint. Sam seems more exasperated by this than anything.
Sam: Seriously, Briggs!
Even funnier, this can happen to Sam himself in the same mission.
Sam: Well, now this is embarrassing.
There's also Sam's severe dislike of former president Ronald Regan. It comes up in Chaos Theory when a North Korean missile is launched at the USS Ronald Regan and he's told he needs to send the missile's self destruct codes.
Sam: Did you just ask me to win one for the Gipper?
Grimm: Dude, what does that even mean?
Sam: Nevermind, you're right grim, I'm old.
One of the briefings for one of the side missions in Blacklist is pretty amusing. Evidently, working for VORON too long will make you...weird.
Grimsdottir: A VORON agent in Chile reached out to one of our people, offering to defect and provide intel on VORON operations in South America. SMI gives this a high probability of being on the level. Apparently our walk-in says he wants to retire and worship the Great Penguin in peace. He...may be a little burned out.