EarthBound 64. This one just breaks my heart even to this day. I know we got Mother 3 eventually on GBA - well, not the US, but at least the game was fan translated and the fact that it exists is enough for me. But EB64 was my most hyped game ever, until it was cancelled. Would've loved to see what it turned out to be and compare it to the GBA game that did get released.
Project Dream - the prototype SNES game that eventually became Banjo-Kazooie on N64. I don't know much about it but this was created by Rare during the height of their greatness. Every game they put out was gold and I have little doubt this would've been as well. Plus I would've loved to see how different or similar it is to Banjo-Kazooie.