Mega Man 2 - Metal Man vs Ys: The Oath in Felghana - The Strongest Foe: The Ys song is quite good, but despite it not exactly being my sort of game, the MM2 soundtrack is both more jammin' and more iconic. Still close.
Final Fantasy Tactics - Antipyretic vs NieR - Shadowlord: Eurgh. Why Hatbot, why? Antipyretic is my nom, and my favorite song from one of my favorite games.... but Shadowlord is my favorite NieR nom by an order of magnitudes. It would probably win against anything else that's come up so far. However, I have to give it to the one I know and love, and have spent many many many many hours listening to.
Super Smash Bros. Melee - Menu 2 vs Rosenkreuzstilette - Luftfest Sleipnir: Speaking of songs I've spent many hours listening to, this one isn't even close for me. Despite actually being my least favorite of the Melee menu themes (despite the bangin' slap bass), Menu 2 has both nostalgia and composition going for it, while the RKS song sounds just... painful to me.
Within a Deep Forest - Adventures vs Valkyrie Profile 2: Silmeria - How Wicked Ruler: It... hurts to vote against my nom here, but god damn is How Wicked Ruler good. Adventures is, while very good, not even my favorite WaDF song, just the most listenable for a contest. How Wicked Ruler is just incredible, though.
Love Live School Idol Festival - Watashitachi wa Mirai no Hana vs Fire Emblem Fates - The End of All:... Okay, for once, this isn't just me kneejerking away from JPop. The Love Live song was MILES better than I expected, but The End of All was just incredible. I literally came back and listened to it again after voting. Way closer than I expected though.
The Legend of Zelda - Overworld vs Secret of Evermore - Hall of Collosia, Chamber 1: Woof. Obviously it's hard to argue with the iconic joy of the original Overworld theme, but... Secret of Evermore music..............
Atelier Violet - Izareya vs Legend of Legacy - Twin Dimension Battle: Izareya wasn't bad... but took a solid 50 seconds to become listenable. I cannot stand the choir synth, which is odd because usually I love discordant stuff. This just didn't work for me I guess. Twin Dimension Battle was just pretty solid all the way through.
Lufia: Curse of the Sinistrals - For the Savior vs Golden Sun: The Lost Age - The Doom Dragon: Yeah okay, no problem with voting against my nom here. Doom Dragon has nostalgia for me, and I love the time signature changes, but it was more of an exploratory nom than something I expected to do well. For the Savior is just kinda great though.