The ending of MGS3 when it was reveladed that The Boss was actually not a villain:
http://www.youtube.com/watch?v=4tE43Daxbb0
And the second one was at the end of Final Fantasy V, the ultra-epic music of the credits ant the party running on the field...it was like a deserving ending after you did a very hard work and it was your reward. It was problably the most rewarding game I have ever finished.
http://www.youtube.com/watch?v=l6ml2Y40PaY (1:35 - 5:50)

Above: still the best game of the year.







