Dr. Mario and Optomon's CV1 hack, Chorus of Mysteries, is awesome in that it changes tiles, enemies, enemy behavior, music, etc. so that it a new game. They even added a new subweapon to replace the stopwatch - the herb, which acts like laurels in that they grant you temporary invincibility for 7 or 10 hearts, forget which. Must warn you, it is HARD. I simply can't remember how to beat the second boss, and I always lose the axe. The game will make you hate Medusa Heads like you never thought possible, but hey! It's a newer old-school Castlevania, and a superbly made one at that.
Also coming up from the dynamic duo is their Dracula's Curse hack, Cadence of Agony. Their goal is to make it into a non-linear Metroidvania, but obviously in the confines of the NES hardware. You start as Richter, and when you make your way around the castle you'll find Alucard, Maria, and... I forget the guy's name, he was the protagonist of CoM and is a DaNasty descendant. Anyway, they will each have unique abilities (Alucard's bat transform, DaNasty Jr.'s wall-climbing) that you'll need to get to new areas. It sounds an awful lot like TMNT3: Radical Rescue, which is not at all a bad thing. Some impressive changes include the ability to go back to previous areas, vertical scrolling in both directions, a map and quick character select on the pause screen (might be the select button), and some bad-ass new music, which includes NES renditions of many Dracula X songs and original pieces. I'm eager to see how this turns out; the exploration of later games combined with the GOOD level design of the old games sounds like a match made in heaven.
Er, those are the main ones I remember. There was one Metroidvania-looking game called Return to Egypt, but I have no idea where it is. Google 'em.