This post was made just for all the topic title neglectors! >:D
Super Paper Mario: I was kind of disappointed that the great and powerful Luigi couldn't be used in the final-final battle of SPM, but then again he'd make it far too easy. With all the "Are they dead?" stuff before reaching the end I was thinking that Mario would be alone in the last battles and the others would appear alive afterward.
Twilight Princess: So many battles with Ganondorf, so many--first with him controlling Zelda, then with Ganon in pig form, then against Ganondorf on horseback, then against Michael Jackson teamed up with Ganondorf, then Ganondorf in a tutu, and then just a duel with Ganondorf. Midna doesn't die she regains her tall princess shape and shatters the mirror!!!!!!!! Yeah it's pretty crazy.
Mario & Luigi: Partners in Time: Princess Shroob had a twin sister! That was really odd, with the big tentacles and stuff. It's arguable that "Shrowser" was the final boss, but that battle, as I see it, was an excuse for saving after the last battle.