Drama
Roy's death scene (Suikoden 5) vs Epilogue (FFT) - I like the epilogue, but it's, well... It lacks resolution. The fact that Ramza's ending isn't confirmed drains it of its full power in contrasting the two heros, and so it relies primarily on the ending of Delita's arc. Meanwhile, Roy's Death Scene is arguably also the end of his arc, but it also adds to several characters, including a bit for the Prince, and that addition pushes this over the top.
Finding Elina (BoFIV)vs Jowy and Riou team up one last time (Suikoden II) - What OK said. I mean, sure Yuna is a far more effective bastard than Gordo, but he's not that much greater of one. At this point, Gordo's been pulling dick moves left, right and centre, and to not only see him pay for it, but to have the two leaders set aside destiny in the middle of a battlefield so that they can curbstomp him. Wonderful.
Style
World Destroyer Orsted (Live-a-Live) vs Opera (FF6) - Very close, but... well... it's a well executed bad end.
Now is the time! (Final Fantasy X) vs Succeeding you, father! (Warcraft 3) - A bit choppy, but a good capstone moment.
Humor
*Wedding (SMRPG) vs The MAN FESTIVAL (SH2)
Stupid Cow (Soul Nomad) vs Corneo's Mansion (FFVII) - I don't know why Square decided to drop the humour from their games (at least until Crisis Core came along) but the dry wit paired with the absurd that they used in 7 and 8 helps make this scene awesome.
I will...VOTE YOU, I will...WRONG YOU!
Leblanc's Back Rub (Final Fantasy X-2) vs Eirika gives Lyon the Stone (Fire Emblem: The Sacred Stones)