Long post ahoy
So, out of curiosity and because such lists existed for other systems on the virtual console, I went and made a list (it's not a big one) of N64 games released in the US by publishers/rights holders that are also putting games on the VC (those being Nintendo, Capcom, Konami, Namco, and Koei). Obviously not every game in this list is going to make it because the trickle, the Wii VC being almost entirely first party games, and general industry politics, but here's what we could possibly expect.
Bolded games are games that should have no issue
Italicized are games that may have issues but could possibly happen to varying degrees of possibility
Games not bolded or italicized are games that won't happen or have been confirmed to not be happening.
Already Released/Confirmed for release
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***Donkey Kong 64***
***Paper Mario***
***Super Mario 64***
Nintendo
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1080 Snowboarding
Banjo-Kazooie- Owned by Microsoft
Banjo-Tooie- Owned by Microsoft
Blast Corps (MS/Rare?)- Who kept the rights to this one?
Bomberman 64- Nintendo published but Hudson developed. Konami's been weird about putting Hudson games on the eShop, so who knows
Bomberman Hero- Ditto
Command & Conquer- Licensing issues with EA, so lol
Diddy Kong Racing- Unlikely due to MS owned characters. DS port is more likely.
Dr. Mario 64
Excitebike 64- Uses licensed materials, so it would need to have that stuff removed or the licenses renewed for them to resell it (which was done for Wave Race 64, but to a much lesser scale)
F-Zero X
GoldenEye 007- Stuck in licensing hell
Hey You, Pikachu!- Would need to emulate microphone, but not impossible
Ken Griffey Jr's Slugfest- Licensing
Killer Instinct Gold- Owned by Microsoft
Kirby 64
Kobe Bryant in NBA Courtside- Licensing
Legend of Zelda: Majora's Mask (Won't happen any time soon due to the 3DS remake, but could eventually happen)
Legend of Zelda Ocarina of Time
Major League Baseball Featuring Ken Griffey Jr- licensing
Mario Golf
Mario Kart 64
Mario Party- Supposed issues with controls
Mario Party 2
Mario Party 3
Mario Tennis
Mickey's Speedway USA- Licensing with Disney
Mischief Makers- Licensing with SquareEnix, probably won't happen in the US
New Tetris- Given Tetris GB was delisted, it appears this won't happen while Ubisoft is publishing tetris games
Pilotwings 64
Pokemon Puzzle League
Pokemon Snap
Pokemon Stadium- Won't happen due to reliance on transfer pak
Pokemon Stadium 2- Won't happen due to reliance on transfer pak
Ridge Racer 64- Likely to encounter licensing issues, but not entirely out of the question
Sin & Punishment
Starcraft 64- Licensing issues from ActiBlizzard. Won't happen.
Star Fox 64
Star Wars Episode I Racer- Licensing with Disney/LucasArts
Star Wars: Shadows of the Empire- Licensing with Disney/LucasArts
Super Smash Bros
Tetrisphere- Same situation as The New Tetris
Waialae Country Club- Licensing issues
Wave Race 64
Yoshi's Story
Capcom
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Mega Man Legends- Voice rights issues have been preventing the PS1 version from being rereleased. Almost certainly will be the case here unless voices are removed.
Magical Tetris- Licensing Issues on multiple fronts, won't happen
Resident Evil 2 (couldn't be released on the Wii VC due to file size, but could happen now unless other technical issues present themselves)
NamcoBandai
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Ms. Pac-Man Maze Madness
Namco Museum 64 (There's nothing technically preventing this game, but the GBA Namco Museum already on the eshop is basically the same game minus Pac-Man)
Konami/Hudson
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Bottom of the 9th- Licensing issues
Castlevania
Castlevania Legacy of Darkness
Deadly Arts
Goemon's Great Adventure
Hybrid Heaven
International Superstar Soccer '98- licensing issues
International Superstar Soccer 2000- licensing issues
International Superstar Soccer 64- licensing issues
International Track & Field 2000
Mystical Ninja Starring Goemon
Nagano Winter Olympics '98- licensing issues
NBA In the Zone '98- licensing issues
NBA In the Zone '99- licensing issues
NBA In the Zone 2000- licensing issues
NHL Blades of Steel '99-licensing
Rakugakids- Was never released in the US but was released in Europe. Could happen.
Star Soldier: Vanishing Earth- Hudson, so take as you will
Natsume
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Flying Dragon
Harvest Moon 64- Has already been shot down over issues with QA/emulation
KoeiTecmo
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WinBack
Other things to note:
-Nintendo previously worked out a deal with Midway to put Crusin' USA on the Wii Virtual console. Midway has since collapsed, so who knows what's up with that license. I'm leaving it off the list for now.
-Quest 64 was published by THQ in the US but Konami in Europe. As THQ is now dead and its licenses scattered into the wind, I suppose it's possible that Konami (or another related party) could work towards getting the game on the VC. It's super unlikely though, especially given the game's sort of unfair reputation.
-On a related note, many of the N64's more prolific third parties (namely THQ, 3DO, Acclaim, Crave, Midway, and Titus) have since gone under. While the vast majority of those games were licensed and wouldn't happen anyway (sorry fellow WCWvsNWO/WM2000/No Mercy fans), it's not entirely impossible for some of the non-licensed games to happen in a scenario similar to Tecnos's library where somebody picks them up specifically to rerelease them. That said, I'm not including any of those games on the list, because it's a suuuuuuuuuuper longshot that will almost certainly not happen.
-I didn't include Conker's Bad Furday and Perfect Dark since Rare nominally self published those (albeit with support from Nintendo) and they'll certainly hit the same issues that Banjo Kazooie/Tooie and Killer Instinct Gold will hit.
-As noted, Majora's Mask is unlikely any time soon because it was just remade and released on the 3DS. Star Fox 64 and Ocarina of Time also have 3DS versions, but those are old enough to where they'll probably pop up sooner. As it stands, the DS port of Kirby Super Star did not prevent the SNES version from getting released on the VC a couple years later.
-While I've labeled the licensed sports games as being unlikely, there's a tiny precedent that would allow them to be released. Tecmo Bowl made it out on the Wii VC after having the player/team names removed, and the same could happen for games like Bottom of the 9th that weren't explicitly MLB/NFL/NBA/NHL/FIFA licensed. That said, due to the work involved with doing that, I think it's best to just assume that they won't show up and then just be pleasantly surprised on the super minuscule chance they do.
-Interplay will probably promise Clayfighter 63 1/4/Sculpter's Cut, but don't believe their lies
Excellent post. One thing it would be nice to incorporate is the list of titles that were previously out on Wii. This doesn't guarantee a Wii U appearance, nor does it account for titles that skipped the Wii (DK64) but have no come to the Wii U.
That's a good point. So, for reference, the games released on the Wii VC were (with the same formatting):
1080 Snowboarding
Bomberman Hero
Cruisin' USA
F-Zero X
Kirby 64
Legend of Zelda: Majora's Mask
Legend of Zelda: Ocarina of Time
Mario Golf
Mario Kart
Mario Party 2
Mario Tennis
Ogre Battle 64
Paper Mario ****Confirmed*****
Pokemon Puzzle League
Pokemon Snap
Sin & Punishment
Star Fox
Super Mario 64 ****released****
Super Smash Bros
Wave Race 64
Yoshi's Story
As noted, any of the bolded games should be able to be released just fine, with the only caveats being Majora's Mask having a recent remake meaning it probably won't be put on there any time soon.
Bomberman Hero was a Nintendo published game and made it on the VC before. Since then, Konami bought and absorbed Hudson. Despite being fully supportive of the VC, Konami has since become weirdly iffy on putting Hudson games on the VC, with the lone exception being Adventure Island.
Crusin' USA, as previously mentioned, made it on the VC before Midway died. It doesn't appear that any of Midway's other games have made it onto the eShop/Virtual console since then, so either their games are now stuck in legal limbo or whoever bought them (most likely Warner Bros) isn't supporting the service. As such, I wouldn't expect Crusin' USA (or Crusin' World, for that matter) to show up again.
Ogre Battle 64 was published by Atlus originally, but the VC release was handled by SquareEnix (who owns the franchise). SE has been dumb about supporting the VC outside of Japan, so don't expect it.
Finally, the big elephant in the room is that Donkey Kong 64 is one of the first 64 games being brought to the WiiU VC, so Nintendo is clearly willing to do more than just release what they already put out on the Wii.
