In short, I'll take any final battle song from every major Mario game I've ever played. That organ piece from SM64 is still one of my favorites because it reminds me fondly of Bach's Toccata and Fugue in D Minor.
I also happen to like Professor Frankly's theme from PM2. Every time I hear it, I picture Frankly's face photoshopped onto a cardboard cut-out pharaoh dancing in rhythm like a cliché Egyptian.