FFI - I have no idea why, but I really like it.
FFVIII - Orchestral Eyes on Me + FF theme + little scene at the end = beautifully epic
FFX - not Suteki Da Ne (which is nice, but not my favorite), but the song in the ending FMV. It's touching and fits the scene wonderfully.

Chrono Cross - You know, the actual long ending. Every single song that plays is a masterpiece.

Original Metroid & Metroid II - both very cheery and upbeat.
Super Metroid - Perfect and triumphant.
Metroid Fusion - It's quiet and rather understated, but it strikes an emotional chord within me somewhere.