If I were to include licensed stuff, it's not a lot. Popeye is the big one.
HAL would have Jumbo Ozaki no Hole in One Professional, New Ghostbusters II, Gall Force: Eternal Story ,and Gozonji Yajikitatin Douchuu. They published Day Dreamin' Davey and Kabuki: Quantum Ninja, but they didn't develop either of those.
Nintendo, meanwhile, has the aforementioned Popeye and its educational Japan only spin-off Popeye no Eigo Asobi, Nakayama Miho no Tokimeki High School (Nakayama being a popular idol at the time, and was co-developed with Square for Japan), and Mike Tyson's Punch-Out!! (NOT HAPPENING).
They published a port of Enix's Ginga no Sannin (JP only), Konami's Smash Ping Pong (which is on the Japanese NSO app), Irem's Kung-Fu and 10 Yard Fight, and Tetris and Tetris 2 (along with Knight Move, another game designed by Alexey Pajitnov for Japan only). They also published several Rare games (which we're slowly seeing, but we are currently waiting on Slalom and Pin*Bot [which has its own license]), Human and Bandai's World Class Track Meet (previously known as Family Fitness Stadium Events in NA and Running Stadium in Japan) and Dance Aerobics, Square's Rad Racer (and Final Fantasy, of course), Enix's Dragon Quest (as Dragon Warrior), and Yoshi's Cookie (developed and published on the SNES by Bullet Proof Software, which might be the holdup on its rerelease. The NES version was developed by TOSE and published by Nintendo). Plus the Mario is Missing/Time Machine games, but those are very unlikely to come back.
I added a couple more to the main list too that I missed in my haste, lol.