When Eragon returns from gathering dragon lore from Brom, he goes to see the as-yet-nameless Saphira, who is still repeating his name, the only word she's ever said at this point. He asks her if that's all she can say, and she replies, "Yes." As always, the key ingredient in comedy is misery; Eragon is thoroughly unamused by her joke, as he's still reeling from the realization that dragons are sapient.
The scene in the second book in which Saphira gets drunk, an event that, on the surface, is hilarious. You have this wise and noble dragon drinking ale by the barrel and generally partying it up. Think about that. You have a dragon. One that is both huge and fully capable of breathing fire. Completely shitfaced. There's no way thiscould possibly end badly. Not to mention that at the end of the scene, she tries to bow. It doesn't end well, as you can imagine.
Also in the second book, Roran is in the middle of leading the village to the Varden, and he's more than a hero for them. They discuss plans to travel by barges, which results in heated arguments. All of which leads to the simplicity of this line (paraphrased):
Roran rose, and the village instantly quieted. They waited, breathless, hoping for another of his legendary speeches.
Roran: It's this, or walk.
Then he went to bed.
In the chapter "The Secret Lives of Ants", Oromis told Eragon to go "listen to the world around him". When Eragon comes back and regales him with tales of ant-heroes, this is probably the most pissed we ever saw him.
The bath scene.
Another great Eragon and Oromis moment, when Oromis has given Eragon some homework: scrolls to read which, according to Oromis, contain information that would be tedious to vocalize. Eragon's only response is, "Vocalize?" Oromis simply adds another scroll to the pile and says, "This is a dictionary."
Eragon meeting Tenga, inadvertently setting him off on a history rant, then quietly backing out the door and sprinting off while his back is turned.
"Its name is Albitr, which means exactly what you think it means. However, I like to call it Tinkledeath, because of the sound it makes when you tap it."
At the end of Inheritance, Angela is knitting a hat. Eragon asks her what's written on it.
Probably not done intentionally, but Galbatorix gets a hilarious line when he encounters our heroes for the first time.
It was inconsiderate of you to attack so early in the morning. I was already awake- I rise well before dawn- but you woke Shruikan. He gets rather irritated when he's tired, and when he's irritated, he tends to eat people.
During the siege of Belatona, Eragon tries to spear soldiers standing on top of a guarded wall. Not only does he miss themcompletely, but the soldiers call him on his failure and laugh at him like assholes. Doesn't last long, as Arya grabs a spear and impales the lot of them.
The entire Missing-A-Scale scene in Inheritance. Comes back in the end:
Anytime the mighty Saphira behaves in a playful cat-like manner.
Eragon's ineptness with politics. This alone should have made it painfully obvious to any reader that he was never destined to become the next king of Alagaësia. One particularly amusing example comes towards the end of Inheritance during the discussions regarding just that matter: who is to be the next monarch. King Orrin of Surda is pushing for the position, but Nasuada is adamant that it should be hers. She offers him certain territories, at which point he starts quibbling over which ones should be part of the deal. At this point, it's obvious to anyone studied in politics that everything is done except the details and that Nasuada has just become the next queen, but Eragon still worries that Orrin is still after the job.
Eragon's reaction to the giant snails, Snalgli. Whether the situation was really all that funny is debatable, but his amusement is infectious.
Eragon's theory regarding the dwarves:
It occurred to Eragon that although the dwarves were the shortest of the races, they built the biggest structures in Alagaësia, which seemed odd to him. Perhaps, he thought, by making such enormous objects, they do not feel so small themselves. He almost mentioned his theory to Orik but at the last moment decided that it might offend him, so he held his tongue.