Fallout 3 is on that list....

But yeah, overrated though the game itself is, I love FF VII's ending.
KOTOR and KOTOR II
Silent Hill 2- There were so many different endings you could get and each one left a huge emotional impact on me. Even the dog one.
If we are talking about final bosses/stages as well, I would put New Vegas on there too. If DLCs count, Lonesome Road deserves a spot.
Shivering Isles, because mantling Sheogorath is just the best thing ever.