Your mileage may heavily vary, but Bond getting shot by Eve. It was such a spectacular failure that it goes beyond being shocking and then become hilarious. Since it was little over 10 minutes into the movie so no one really expected him to actually die anyway.
During Bond's assessment:
Psychologist: Day. Bond: Wasted. Psychologist: M. Bond: Bitch.
After all Bond's been through, he still looks at his most pissed off following the explosion of his Aston Martin.
Silva's entrance via helicopter, loudspeakers blaring music like he's Colonel Kilgore. Its even more hilarious when you pay attention to the lyrics of the song which are horribly ironic in the context of the situation and the film.
After Bond throws a knife into Silva's back, Silva's reaction is more annoyance than anything else.
Fridge Brilliance kicks in when you consider that just seconds earlier, Silva was holding a gun to his and M's heads, trying to induce her to shoot them both with the same bullet. He wasn't planning to walk away from this alive, so when Bond stabs him, it's very easy to read into his exasperated grunt a layer of "Look, I get it, buddy, but you couldn't at least have let me watch her bleed out first?"
He almost rolls his eyes outright when Bond falls into the moor wrestling the henchmen that was about to shoot him. "Does he have to make everything difficult? Forget it, moving on."
All the scenes involving M's porcelain Union Jack bulldog.
Bond: The whole office goes up in smoke and that bloody thing survives?
Bond's flabbergasted looks at the Komodo Dragon.
Even better is that when he first notices the dragon, he apprehensively points at it, as if he's trying to tell the other guy (whom he's fighting) to watch out for it.
Bond, to pursue Silva, runs after the departing Tube train, leaps onto the back of the last car and gets the employee in the rear cab to let him in through her door:
Bond: Health and safety. Carry on.
Then we cut to two passengers on the platform. The man quips, "He's keen to get home!"
Q: There should be a service door to your left. Bond: Got it. [Tries door] It won't open. Q: Course it will. Put your back into it. Bond: Why don't you come down here and put your back into it? [Sees train approaching and he's stuck in the tunnel, right in its path] Oh good. There's a train coming. Q: Hmm. That's vexing. Bond: [After shooting the lock and getting through the door just in time] I'm through. Q: *flustered* T-Told you.
Kincade shows off his shooting skills to Bond but Bond tells him to stay behind. Kincade's response?
Kincade: Try and stop me, you jumped up little shit!
While Bond and M are driving in the Aston Martin.
Bond: "Are you going to complain the whole way?" (Opens the gear stick knob to reveal a red button).
Just after a mook snatches Bond's signature, handprint-locked gun:
Bond: Good luck with that.
Bond's reaction to Eve favouring desk work instead of resuming field duty:
Bond: If it's all the same to you, I feel a lot safer.
Q and Tanner are secretly trying to lay a trail for Silva to follow Bond to Skyfall. Mallory shows up, they panic, and he tells them to carry on, even giving them advice (send the trail up the A9, a major trunk road, because they'll be able to track Silva with traffic cameras). The two are left in a state of shock. It's made all the better by the fact that Tanner's drinking throughout the entire scene.
When Bond introduces M to Kincade, he hears her name as "Emma". She doesn't bother to correct him.
The poor Mook who gets dragged away by a Komodo dragon at the casino in Macau. It's quite all right, Komodos don't eat people. But at the end of the scene, as Bond walks away, you can hear another loud howl of pain from the mook while the keepers go get him, who is being shown how much the dragon dislikes having his personal space invaded.
When Bond is at the Casino bar, he notices the girl making his drink is shaking the drinks without having to be told to. Bond smiles in contentment, muttering "Perfect."