-Bionic Commando. Capcom wanted to do it, but Nintendo outright refused to let them.
-Contra: for whatever reason, the most widely-beloved entry in the entire series has never been released on any service (the arcade game was released, but I never thought that it was as good).
-The Capcom licensed games: Little Nemo, Chip and Dale's 1-2, Ducktales 1-2, Talespin, Darkwing Duck, Willow, etc.
-Tmnt 1-3. The first game WAS released on the Wii VC, for a limited time and at somewhat of a premium price. The license has shifted hands since then.
-The MacAdventure series (Shadowgate, Deja Vu, Uninvited): now, these games COULD be released, seeing as how Shadowgate was released for 3DS in Japan. I doubt that it will happen, though.
-Games made by companies that either no longer exist, or have left the industry. Vic Tokai--who did Clash at Demonhead, Golgo 13--for example.
I really don't think that there is a way for them to make the NES exciting again. Between the Wii/Wii U/3DS VC and the NES Classic, they've sort of overplayed their hand. There isn't much left that they could realistically release that hasn't been released a million times over. I'll still beg for a rerelease of Nightshade, though.