Heh, the only game on this list actually made by Nintendo itself is Majora's Mask... I don't really understand your rules for how you "reduced" the list, though. Given that most of the games aren't by Nintendo itself, for the N64, dividing it just by "first party/third party" is problematic.
On this list, first parties include: Nintendo, Nintendo EAD, NST (Nintendo Software Technology), HAL Laboratory (I'd call it one, but some consider it second party)
Second parties include: Rare, Left Field, Ambrella (according to Wikipedia)
Third parties include (titles of theirs published or distributed by Nintendo): Paradigm, Midway, Camelot, Hudson, Lucasarts, Newcom, Treasure, Angel Studios, Mass Media, Looking Glass Studios
So really, what makes most sense is to divide it by how likely each game is to show up. Licensed titles should go first, for the ones that might have the most difficulties (Lucasarts games aren't really licensed! I mean, licensed to themselves? What's the point of noting it...).
Titles added are in bold.
Licensed said:
Tetrisphere - H2O [from The Tetris Company]
The New Tetris - H2O [from The Tetris Company]
Goldeneye - Rare
F1 World Grand Prix - Paradigm (Published by Video System but distributed by Nintendo in the US and Europe; Published by Nintendo in Japan)
Kobe Bryant in NBA Courtside - Left Field
Major League Baseball Feat. Ken Griffey Jr. - Angel Studios
Waialae Country Club: True Golf Classics [licensed?]
Command & Conquer - Looking Glass Studios [from Westwood] (supports Expansion Pak)
Ken Griffey Jr's Slugfest - Angel Studios
NBA Courtside 2 - Left Field
Mickey's Speedway USA - Rare [from Disney]
Ridge Racer 64 - NST [from Namco]
Starcraft 64 - Mass Media [from Blizzard] (supports Expansion Pak)
The NHL & NHLPA Present Wayne Gretzky's 3D Hockey - Midway [licensed] (Midway developed and published in the US, but Nintendo published in Europe and GameBank in Japan)
Of these, Ridger Racer 64 is a first-party title and I would say is very likely to show up eventually. Command & Conquer might be possible as well, though Looking Glass Studios' closure years back might complicate things there, if they had rights instead of just Westwood (now EA). The two Tetris games remain possibilities as well.
The rest we probably will never see.
Likely to eventually see said:
Pilotwings 64 - Paradigm
Diddy Kong Racing - Rare
Cruis'n World - Midway (note: Cruis'n Exotica was published by Midway, not Nintendo, so it was removed from the list.)
Mario Tennis - Camelot
Mario Golf - Camelot
Mario Party - Hudson
Mario Party 2 - Hudson
Mario Party 3 - Hudson
Super Smash Bros. - HAL
Excite Bike 64 - Left Field
Dr. Mario 64 - Newcom
Pokemon Stadium - HAL (Supports Transfer Pak)
Pokemon Stadium 2 - HAL (Supports Transfer Pak)
Donkey Kong 64 - Rare (Requires Expansion Pak) ("Rare" published in the US, Nintendo published everywhere else)
Legend of Zelda: Majora's Mask - Nintendo EAD (Requires Expansion Pak)
Pokemon Puzzle League - NST
Star Wars Episode I Racer - Lucasarts (Published by Lucasarts, Distributed by Nintendo in the US; Published by Nintendo elsewhere)
Star Wars: Rogue Squadron - Lucasarts (Published by Lucasarts, Distributed by Nintendo in the US; Published by Nintendo elsewhere)
Star Wars: Shadows of the Empire - Lucasarts
Bomberman 64 - Hudson
Mischief Makers - Treasure
Bomberman Hero - Hudson
The last six titles are ones that the original list didn't put in the "likely to see" category, for whatever reasons, (because five of the six are third party developed? But so are most of the rest of the games on the list... and that still doesn't explain Pokemon Puzzle League's omission.) but they should be there.
Midway's only VC game so far is Cruis'n USA of course, and Lucasarts hasn't released anything on VC yet, but I would be surprised if they don't eventually release some of their N64 Star Wars stuff. Rogue Squadron was added because it had a similar publishing arrangement as the later Episode I Racer.
Unlikely to ever see said:
Killer Instinct Gold - Rare
Blast Corps - Rare
Banjo-Kazooie - Rare
Banjo-Tooie - Rare
Hey You, Pikachu! - Ambrella (second party) (Microphone)
Perfect Dark - Rare
Jet Force Gemini - Rare ("Rare" published in the US, Nintendo published in Europe & Japan)
Conker's Bad Fur Day - Rare ("Rare" published in the US, THQ in Europe, Nintendo in Australia)
For the last category, Hey You Pikachu requires a microphone and the rest are Rare games.
Note -- while this only originally included some of Rare's 13 N64 games, really, they all should be listed, because I think that even the titles that were technically "self-published by Rare" on N64 were actually done by Nintendo, just with Rare's logo on them. Either way, they should all be together. All except the two DK games go in this category.
There's also the N64 version of
Glover, which was published by Hasbro here, but published by Nintendo in Europe.
There's only one more to mention...
Ogre Battle 64, published by Nintendo in Japan but Atlus here, and now an ignored part of Square-Enix's library. We probably will never see it, sadly.