Ones I can recall off the top of my head that weren't mentioned here;
1) Sonic 1 Megamix - still WIP but even in the known publicly available builds, we got Sonic 1 ported to Sega CD as well as a bunch of remixed Sonic 1 levels with multiple player characters, music changes, new mechanics, etc. Sonic hacks are generally impressive, and I could probably fill a list with Sonic hacks alone (the infamous Sonic 2 XL is also worth a mention for technical ability, even if the subject matter is a bit of a joke.) but it's simply hard to top Megamix for it's scope.
2) Super Mario Bros. 3mix - I'd say this gives Adventure a run for it's money in technical accomplishment. Player select with three player characters, many engine tweaks, levels with gimmicks inspired by latter Mario games, probably the most impressive being Mario Galaxy-esque gravity mechanics, and a nice new soundtrack, all taking cues from the broad history of Mario.
3) BS Zelda Mottzilla Patch - Take BS Zelda Map 2's ROM, a game that doesn't work on a regular SNES as it is and then get it to work, essentially doing a portjob all things considered. Then combine it's map data with one from the Map 1 one so you can play either of them in a single ROM, essentially making a 2-in-1. Rewrite the save system from scratch, add an animated title screen and new save menu (again, all while keeping real hardware compatibility), and have the game play out in a manner reasonably close to the original broadcast, all while having as few bugs as possible. Satellaview ROM hacks deserve props in general, because many of them require this kind of work to be done for ease of playability, and I'd suggest the Radical Dreamers fan translation for many of the same reasons. Watch out for the MSU-1 BS Zelda hacks that may come around publicly soon.
4) Final Fantasy VII Famicom/NES Pirate fan translation - actually sorting through all that junky pirate Famicom data and making not only a nice translation, but a more generally competently-coded Famicom game.
Also, pretty much any translation successfully carried out on the Famicom Disk System is a small miracle considering how much of a pain that is to deal with. If Famicom Tantei Club Part I, Yuuyuuki or Time Twist ever get done, those would probably be up here in a flash. I'd imagine earlier disc-based material would have similar issues leading to any successful project being impressive on it.