I was sort of hoping to get something more than a link to some roms. I wanted to see if anyone else had come across a hobby game they felt had the same level of polish as Cave Story
I can't provide links at the moment, but I know that Kenta Cho (ABA games) makes some really nice shooters. rRootage and Noiz2sa are classics. There's also Torus Trooper, and my personal favorite, Tumiki Fighters (defeated enemies stick to your ship, adding their firepower to yours. It's really neat.).
if you google "doujin shooter" chances are you'll find plenty of freeware shooters in a similar vein.
Pixel has also made a couple of other pixelly games, if you want to search out his website.
If you have a mac, lurking around idevgames can wield any number of free/ in progress games. Macupdate.com usually has most of the mac games out there, freeware or shareware, too.
Abuse has been released for free. Check out
Liberated Games for other commercial games that shared the same fate (like the first two GTA games and Bungie's venerable Marathon series).
Spend a couple of hours roaming through sourceforge or
games made using sdl(most of them are freeware).
N, the ninja game, is freeware and is one of the best lode-runner type games out there. There's also Enigma, which is based on the old oxyd games by dongleware (search for enigma and oxyd on google and you should find it).
Does that help?