I'd change the Layton 3 ending, I won't make Claire survive since it'd kill the actual ending, but I'd make Bill Hawks pay for all the lame stuff he did, he'd go to jail.

What about you?

I'd delay Red Steel 2's ending a good 6 hours or so :)

Id make Black Ops' actually make sense

I'd kill Elena in Uncharted 2
I'd slightly alter the way Faldo kills himself at the end of Valkyria Chronicals

Not a game but still-
I'd kill Cloud at the end of Final Fantasy 7 AC

Oh. I wouldn't dare to change Red Dead Redemption's ending. But I would gladly hug John Marston before it happens. He's been like a father to me.

This was the stupidest moment in the entire game, and that's saying something.

Mercenary Force for the original Game Boy. Really, just about anything less depressing will do.

killzone 2 - I'd make Rico kill himself for his unbelievable stupidity and general annoyingness.

Other than Valkyria Chronicles which has been mentioned, I would say Zelda: Majora's Mask as I wanted to know if/how Link found Navi.

I also would say the 'bad' ending for Metal Gear Solid, but that was before I saw the 'good' and what is considered the 'correct' ending

ditto.