Star Fox 2 is the big one for me. The game was shown at CES in a completely beatable form, and a copy available on the internet is 95% finished (although I'm not condoning that), it really is something they could realistically finish patching up and have a semi-big release to the Rev Virtual Console. It presents a nice evolution to the series, with the three different types of Arwings and their transforming modes, and a sort of "always running" map/battle that you had to keep track of. Some people have mentioned short times finishing it, but it's still enjoyable, and is much longer and more complicated if you tackle a higher difficulty (it's not just going to up the damage level or something).
Really, the only reasons it didn't see release were 1. It was close to the SNES's end, and Star Fox 64 became a priority title for the N64, and 2. The Super FX-2 chip would've made for costly carts. (Although a few games were released that used it, I think SMW2: Yoshi's Island did.)
