Yoshi's Story is the winner! Thank you very much to everyone who voted. Tentatively, we'll plan to discuss the game on Episode 214, so start now if you want to play along. I'll create a separate thread for Yoshi's Story discussion.
Personally, I'm a little surprised by this result (originally thought Banjo, Ogre Battle, or Perfect Dark might win), but I'm also excited to play this game for the first time. It seems like a good fit for RetroActive: overlooked, somewhat controversial, and thankfully, not too long! ;-) It's also a neat tie-in with Kirby's Epic Yarn.
For those wondering about how the voting progressed, it was a virtual three-way tie for the first week or so, with Yoshi slowly pulling into the lead over the second week. Since there's a tie for second-place, both Ogre Battle 64 and Perfect Dark will return in our second-chance poll, which should be coming up very soon.