I'd say the Super Mario Infinity hacks are longest. Sure, some other hacks have a lot of levels, and perhaps even more of them, but these hacks have levels with what, about 100 rooms later in the game? To be fair though, the second game probably does go on for too long if the videos I've seen of it are accurate, it throws in enough 'man behind the man' situations to rival Brawl's Subspace Emissary.
Another long hack I don't think has been mentioned is Demo World the Legend Continues. Pretty long game, and rather confusing to beat 100%.
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As for Mario's Nightmare Quest? Well, it's currently on Fusion Gameworks, ROM Hacking.net or the GCN at the moment.