The Sky is Falling, the Sky is Falling
The word "Skyfall" is a mystery. It's first crooned by Adele in the opening song, making it into a Chicken Little-like portent of foreboding disaster. Later, the word is dropped in Bond's psych eval word association game.
EVALUATOR: Skyfall. [pause] Skyfall.
Bond doesn't want to hear about Skyfall, but what is it? A secret nuclear missile program? A failed mission? His secret screen name? It's a touchy subject, whatever it is.
It's only toward the end of the movie that we learn that Skyfall is Bond's childhood home. The front is guarded by a stag, like Harry Potter's patronus cast in bronze. But the whole place is grim and gloomy, prompting M to comment, "No wonder you never came back."
If Skyfall were ours, we'd spruce it up into a nice B&B, but Bond has no desire to make the estate cozy: it's a place of grim childhood memories. We're led to believe that Bond's parents were killed there, while young Bond hid underground. That's more than enough to make a person turn away and never come back.
But Bond is forced to return, luring Silva to Skyfall for the final showdown. The standoff wipes out memories of the past for both M and for Bond. For M, Silva is a person she may feel guilt or remorse about, and he is eliminated. For Bond, those complicated feelings toward his childhood home go up in smoke when the place literally blows up.
While M might be conflicted about past decisions, Bond displays no such inner turmoil about rigging his family estate with explosives: "I always hated this place," he says.
Bond deals with the past the best way he knows how—by sending it up in flames and starting over. He is ready to put the past behind him, and it's easier to do that when the past is a literal pile of ashes. Maybe Bond isn't actually crying at the end—it's just soot in his eyes.