ShogunGino said:
Ogre Battle 64,
...
the very excellent Resident Evil 2 port,
I noticed how terribly grainy the graphics were due to the data compression needed to force-fit them into cartridges. Also the sound in RE2 tended to glitch, causing it to sound very echo-ey. They were apt demonstrations of why the other console makers at the time had switched to CDs. (that and discs were much cheaper to manufacture) If only something akin to today's chips were available back then... Oh well.
I'll add Superman 64 to this list. j/k
In all seriousness, LoZ: Majora's Mask.
"Who underrated this game," you ask? Nintendo themselves apparently. They could remake it for the 3ds like OoT, but currently they're only "considering it" despite plenty of demand. I honestly don't know wtf they're basing their decisions on anymore.