When Anakin and Obi-Wan argue about how many times the young apprentice had saved his master.
Anakin: You owe me one, and for not saving your skin for the tenth time.
Obi-Wan: Ninth time. That business on Cato Neimodia doesn't... doesn't count.
Made even funnier in the novel Labyrinth of Evil, when we see just what that "Business" was. Obi-Wan unintentionally got high and Anakin helped him finish off a group of battle droids that were attacking him.
Virtually all the snark from the droids at the beginning of the film.
When General Grievous snatches two lightsabers out of a poor downed Battle Droid's hands.
Battle Droid: You're welcome.
You practically feel the snark from that one. It passes by Obi-Wan and Anakin as it gives their lightsabers to Grievous and even says 'Excuse me.'
The scene where Anakin heckles Grievous.
General Grievous: Anakin Skywalker. I expected someone with your reputation to be a little... older. Anakin: General Grievous... you're shorter than I expected. General Grievous: Jedi scum! Obi-Wan: He has a job to do, Anakin. Try not to upset him.
Obi-Wan's total lack of reaction to everything going to hell during the battle of Coruscant.
"Not to worry, we are still flying half a ship."
For that matter, the entire Coming In Hot scenario with increasingly large portions of the ship bursting into flames and/or falling off as Anakin brings them in for a forced landing. What should be a terrifyingly catastrophic scene (all of those chunks of the ship are falling over a very large city, and the ship itself takes out several buildings at the spaceport when it ditches) ends up being hysterically funny, thanks to Anakin and Obi-Wan's deadpan commentary.
From the novelisation: Obi-Wan and Yoda are considering how they will get back to Coruscant post-Order 66, and look dubiously at the small one seater spaceship Obi-Wan arrived in.
Obi-Wan: I suppose... if you don't mind riding on my lap...
The novelization has a number of darkly funny moments whenever Grievous is forced to put up with Nute Gunray. Most notably: "Grievous resisted his natural inclination, which was to boot the Viceroy so high he'd burn up on reentry."