Invisible Full Moon by ZUN, from Touhou 8 - Imperishable Night, Stage 5 boss theme (Reisen's theme). There are a few others and they are the Fire Emblem main theme song of many of the series, and then of course Seiken Densetsu 3 (Secret of Mana 2) Sacrifice Part III.
"Castle Bleck" from Super Paper Mario. SPM is an odd game in the Paper Mario series with its surprisingly mature plot, different gameplay and its much more abstract art-style. The music in this game is very distinct too and full of fantastic tracks, with this one being my favourite. It's the music for the final world of the game and it's an extremely gloomy and mysterious sounding track. It's super interesting musically and in its choices of instrumentation.
Fire Emblem games generally have good soundtracks imo, so do Pokemon and Dangan Ronpa. Honestly whenever I'm on the fence about buying a game I listen to a few of its tracks to determine if it's worth getting or not, a good soundtrack can add a lot to the experience.