Spiral of Erebos is one of my favourite tracks in video games ever. The dungeon was very straightforward, but the track is fantastic, and the fact that it persist in battles is great. I would also like to bring up the Sun Fort at the end of Trails from Zero as well, when A Light Illuminating the Depths starts playing and you see the cast run into the dungeon, it's such a fantastic buildup.
13th Street from Castlevania: Portrait of Ruin - It plays a remix of Iron Blue Intention, a fantastic track, and the stage itself is fantastic, it's a late afternoong-evening Victorian-era city infested with monsters, almost like an apocalypse scenario. It may sound a bit silly to say, but the background of this particular map always fascinated me.