When first controlling his avatar, Jake's tail surprises him when he notices it over his shoulder. When he turns around to look for his tail, it knocks medical supplies off a table.
This exchange between Grace and Sully while the latter is first entering his chamber:
Grace: "Just relax and let your mind go blank. That shouldn't be too hard for you."
Sully: "Kiss the darkest part of my lily-white (gets cut off)."
For a serious character, Grace gets more of these than you'd expect:
If you know any scientists, this line is hilarious. Grace is carried, mortally wounded and half-conscious, to the Tree of Souls that she had been wanting to research for years:
Grace: I need to get some samples...
Grace's indignation at Jake not being experienced anywhere in science can be hilarious.
Grace: They're just pissing on us without even giving us the courtesy of calling it rain.
Crowning Moment of Funny? Reportedly, Sam Worthington, Jake's actor, emailed Entertainment Weekly with his own ideas for a sequel:
Sam Worthington: Jake should have abused his avatar and be fat and unfit and demand Neytiri to get him a beer.*
A hilarious moment from the deleted scenes of the collector's edition: Jake wakes up from his Avatar and goes looking for the others (Grace is outside) and he turns a corner, and Trudy and Norm appear to be in the middle of a lovemaking session. Then Jake's voice over crowns the funny "Norm's attitude has improved lately."
An even more hilarious moment from the deleted scenes occurs during the meal at the campfire:
Jake: These rock. What are they?
Ney'tiri: Teylu.
Jake: Teylu?
Neytiri: You call [it] beetle larvae.
Beat
Jake: Well, that's some damn fine Teylu. Just like Grandma's Teylu.
The Sturmbeest Hunt had this gem of an exchange:
Jake: Hell yeah!
Neytiri: (who has no idea what it means) Hell yeah!
Parker Selfridge's reaction to being lectured by Grace (presumably for the umpteenth time) about having just bulldozed something holy is hilarious.
Grace: Those trees were sacred to the Omaticaya in a way you can't imagine.
Parker: Oh, you know what, you throw a stick in the air around here, it's gonna land on some sacred fern for Christ's sake!
Likewise, Parkers retort to Graces lecture after bulldozing the Tree of Voices
Grace: That's more connections than the human brain. You get it? It's a network — a global network. And the Na'vi can access it — they can upload and download data — memories — at sites like the one you just destroyed.
Parker: What the HELL have you people been smoking out there? They're just goddamn trees!
Jake convincing the Na'vi to teach him.
Moat: It is hard to fill a cup that is already full.