Someone already beat me to Link's Awakening, but good on 'em for bringing it up. So!

Tekken 4. Not as bad as people think. It's actually a fun fighter. It just doesn't stand out like lots of the others in the series.

Tenchu: Fatal Shadows. Okay, so maybe Tenchu isn't super popular. Still, this game was largely forgotten in the series, and I think it did a lot of neat, fresh things in it's story telling. Plus the game plays well.

Star Fox Adventures. Yes, I liked this one. Yes, it was cutesy and light hearted. I really had fun with it. It still had Rare polish with Nintendo backing. I was excited for a Star Fox themed Zelda adventure and I was largely pleased with the results. At least it tried something new. Almost every other entry in the series is basically the same game re-hashed. Same story, same basic plot, and Nintendo is scared and/or doesn't know what to do with the story/series. This one tried to be different. smurfin' sue me, haters.

Final Fantasy 10-2. This one seems to have become more acceptably popular over the years, but I played the bejeezus out of it from the beginning. Loved the gameplay, enjoyed the light hearted atmosphere, laughed at the fun characters, rolled my eyes at the stupid story. Final Fantasy 8 is a close second.