I think Halo:Reach had a good ending due to the fact that everyone died and you weren't going down without a fight. *POSSIBLE SPOILERS* I also like the twist ending of COD:BlackOps where we learned that Reznov was never with Mason all that time and how Mason was involved in the assassination of JFK.
The whole story in Super Paper Mario was amazing and very well-written. I like the twist involving Luvbi in chapter 7. Also, the whole motive behind Count Bleck's actions is existent and makes the story better. And the ending is so sad...
Ultimate spiderman. One of my favorite video games. Your thinking "Oh duh, we fought venom 3 times, he is going to be the final boss." Final boss: Spiderman turned into carnage, fight carnage as venom.
I loved the ending of Zelda: Twilight Princess. I guess I love the bittersweet open ending. It feels so real, since perfection could not be achieved, but the future seems limitless and bright. It also helps that awesome Zelda music is playing in the background.
I love the ending of Wind Waker the best out of all Zelda endings, because it's so emotionally powerful. At least to a devout Zelda fan like myself. Not only do we see our beloved Hyrule Field and our old memories again, they're flooded and lost forever. And Ganon is by far the most human and relatable that he's ever been.