Pretty much everything Psycho says, especially with the over-the-top British slang he uses.
Im British, you muppet!
During one of the docking station missions in the end of the first game, one of the marine soldiers accidentally shoots you, thinking you were one of the aliens. His response? Aw, shit! I thought you was one of those creatures!
In Crysis 2, there is just something funny about the prompt coming up in front of a Ceph Tick saying "Press to Squish". Not crush, stomp, or flatten. Squish.
In one of the final missions, you are tasked with "rescuing" Hargreave and killing Commander Lockhart. Lockhart's quotes become annoying after a while (as they're repeated until you reach him), but his hammy performance keeps it amusing:
And the kicker (no pun intended), should you choose to Power Kick said toilet, you get this.
The Marines constantly referring to Alcatraz as "suit guy".
Legion reveals that Alcatraz is a snarky little bastard. The highlight has to be when he Lampshades DARPA's decision that, in their opinion, after spelling out that the Ceph were likely aquatic-based beings, the best way, to take them down, was to drown them.
In the opening of 3, Psycho says he's "always been a team player". Cue Prophet analyzing his memories, which describe him as "renegade", "out of control", and similar ideas. "Conclusion: Incorrect Analysis."
This troper found Prophet's tone of speech when Psycho use an abandoned fuel-carrying train to plow through blocked path early in the game amusing.
At one point in the third game, Psycho and Prophet are sneaking through CELL-occupied tunnels, with Prophet constantly being berated for making too much noise. Eventually, they come to a place where they must split up. Psycho starts climbing a ladder, only to knock off a rung and send it clattering to the floor:
Psycho: Do you think they heard that? * the sound of multiple safeties being switched off comes from the next room* Psycho: ... I don't think they heard that.
During the beginning of the mission to destroy the hydroelectric dam, you can eavesdrop on a squad of CELL soldiers as they prepare to hunt for Prophet and hear this gem:
CELL Commander: Listen up. Intel suggests - Ah, fuck that. We are 100% goddamn positive the tin man is in this quadrant. You know his MO - the dam will be his primary target. We are deep inside the Hades radar shadow. That means no guns on this one. It's down to you assholes. So stick to the plan, don't fuck around, and cover each other. Any questions?