Suikoden I vs Final Fantasy 6 - Tempted to vote Suikoden 1 so I don't agree with Dune or NEB here. Nonetheless...this is one where I think both work, both fit equally, but the overall quality and variety and synthesis of instrumentation favours FF6 massively.
Atelier Totori vs Fate/Stay Night - I know nothing really about these two, so in-game context is fairly minimal. That said, Totori feels more fitting.
Tales of the Abyss vs Dark Souls - Wow. Uh...Dark Souls fits really, really well. Probably moreso than TotA here, honestly. Dark Souls is the same style, but...damned if it isn't perfect. Having said that...I think variety of fit works here. TotA balances it's styles better and does more than, as Snowy-poo put it, "dusky haunted cathedral", so I'll vote for it here - but man, it's not like that style is BAD or anything. It just provides less external validity than TotA, and I'll be happy to see either advance.
Castlevania Symphony of The Night vs Wild ARMs 1 - ...again, I have a lot of love for WA1 (it does the "western" theme the second best of the series, after WA3), but SotN's music SCREAMS "Dracula!" so well.