Another Metroid 2 Remake. It was fantastic, and made Metroid 2 actually playable

Project M. I thought it played better than Brawl.

Chrono Trigger: Crimson Echoes. It was a sequel to the original, using assets from the 1st one. I watched the full playthough of it, and it seemed really interesting and rather dark. Sadly it got a desist from Square and that was the end of it. I really wish it had been finished at least.

Another one that looks promising it Mother 4, which has been rebranded to avoid the desist from Nintendo. It looks like a promising sequel to a Mother game, but still hasn't been released. Hopefully it lives up to the Mother name.

Abobo's Big Adventure. Basically a love letter to the NES:

http://abobosbigadventure.com/fullgame.php

Needs Flash, but totally worth it. You can also download it, and with a donation youll get some extra chapters with Abobo's son

I dunno, I'm sure one of the thousands of Pokemon fan games has to be good right??
Seriously that franchise has more fan games then basically every other franchise combined.

I agree with this one. That remake is better than any Metroid game Nintendo has made since the first Prime.