The Reveal near the end of Jak 3. As it turns out, the Precursors, a god-like race responsible for the creation of the world are ottsels. The reaction shot, which includes Veger dropping his cane and Jak's famous "Oh my God" are what really clinch it as a CMoF. According to the Making Of extras, the guy who animated that scene begged to do so once he learned about The Reveal.
There's a lot of subtle things that makes this scene hilarious. Count Veger giving Jak an Eye Take to make sure he is seeing it too. One of the Percursors is trying to move the game's camera to protect their identity. Then there's comeuppance: while the Precursors were still speaking through their Energy Being avatar, they offer to turn Jak into one of them until Veger shows up with a gun demanding that HE receive the "honor", prompting the avatar to say "Be Careful What You Wish For..." One reveal later...
There is a scene in the PSP spinoff that goes like this:
Erol: Who called you?
Daxter: Your boy, y'know, Captain Xi-xi-ximon... Rupert... tikjakmos...
Erol: Nice try. That call didn't happen. [beat] Captain Rupertikjakmos is on leave this month.
"I... AM PECKER!" Even funnier about Pecker is that he's voiced by Chris Cox!
Pecker: Yes, I know. My mother, she was... very vindictive!
The part in Jak II where Daxter gets drunk off his ass is hilarious! "I LOVE YOU, MAN!"
Whenever Pecker and Blitz are on TV in Jak X is hysterical.
The very fact that both can be chosen as pilots. Despite being unable to reach the pedals.
There's this exchange between Jak and Daxter while doing a job for Krew in Jak II.
Jak: Where would you be without me, Dax?
Daxter: Well Jak, I probably wouldn't be two feet tall, fuzzy, and running around in a sewer without a pair of pants... God, I miss pants.
There is a part in Jak II when Jak and Daxter had to gather up three MacGuffins. The cutscenes when you retrieve them are all amusing, but the funniest is the one where Daxter grabs a tiny gear off a giant machine that has a lot of moving parts but no apparent purpose. At first, nothing happens, but as Daxter turns and starts to walk away, the machine stops and falls apart. A cheerfully oblivious Daxter then says "They'll never know we were here." Even funnier when Jak tries to tell him off, but a gigantic cog rolls past him, and causes him to blank out for a second.
Early in Jak 3, Jak is approached by Seem. Eventually, this exchange happens:
"Don't step into the light, Jak! DON'T STEP INTO THE LIGHT!"
"Well, uh...better you than me."
"Say good night, Jak!"
"This is what happens when they drop my name from the title!"
"You did that on purpose, right?"
"Where are the moves, man? I'm wondering, where ARE they?"
The quote at the end of the final boss of Jak 1 where Daxter debates on using white Eco to save the world or change him back
Any scene involving Daxter and Tess in Jak 3. Not just the pair being nauseatingly sweet with each other, but also Jak's reactions at their antics.
Jak: Oh, please! Could you two take it outside?
Daxter: You need a hug, Jak? 'Cos we've got plenty to go around.
Daxter getting blasted in the face with grummy water in Jak II.
Torn using the Naughty Ottsel figure as a final decoy to get a tracking missile off J&D's backs in Jak 3. Daxter's mortified gasp tops it off.
Daxter: (gasp) My beautiful mug!
Daxter in Jak 3 after he blows up the barrier from riding the missile. We see him get up from a huge explosion, he casually dusts himself off and goes to walk away — BAM! Hit by a falling piece of rubble.
Ashelin after it is revealed everyone has been played by Rayn.
Torn: "Who would've thunk?"
Ashelin: "Well, if you'd all been thinking with your... heads."