Your Most Wanted Prototypes?
I've enjoyed researching the prototype scene and supporting those who've sought to preserve this part of history in video games.
Now as far as unreleased games go, or even stuff that does not resemble its commercial counterpart, my list goes like this:
Dragon Hopper (Virtual Boy)
This was to be an action-RPG for VB ala Zelda. Since it's a first party title there's no way it wouldn't have been good, and what we know from the screenshots seemed very promising. Ironically, there is almost no clear, precise footage of the game in-action. I really hope Nintendo saved a copy of this, and if not by official means, then by some generous collector we will see the game someday.
Twelve Tales: Conker 64 (N64)
This game went on to be Conker's Bad Fur Day but as we know, began its life early on as this cutesy, Banjo-Kazooie type of platformer before spending a few years in development hell. While the finished product was amusing, the original, despite criticisms that it would appear too much like other N64 platformers, was too massive and different not to be curious about it.
Sonic the Hedgehog (Genesis/MegaDrive)
The early incarnation of this Genesis classic is one of the few betas in its series to remain undiscovered. Probably as interesting as Sonic the Hedgehog 2 beta, I look forward to seeing this surface provided copies are still extant.
Metal Max: Heart of Gold (Dreamcast)
This cult series, one of the few examples of a non-linear japanese console RPG, would have been more numerous had not several of its titles fallen into development hell. The Dreamcast one in particular promised a more romantic plot, but would remain faithful to the formula.
Sim Refinery (PC)
As a person who has a soft spot for Maxis and their contribution to video games, this one peaks my interest a bit. Developed as an educational aid for the Chevron company, you managed an oil refinery. Never released to the public, it may still manage to see the light of day through some means. I doubt, however, that those means will be official, possibly because it gives away some secrets as to the Chevron trade.
Super Dog Booby (NES)
This game was previewed a few times in japanese magazines but disappeared. The name is hilarious, but the actual gameplay does not involve boobies. Instead, you play a dog guarding a baby from hazards, ala Buttons and Mindy from Animaniacs.
Other notable mentions:
Dead Pheonix (Gamecube)
This rail-shooter by Capcom was to be released among their "Capcom 5" series. A prototype was shown and seemed promising but for some reason it was cancelled.
Sonic Adventure (Dreamcast)
Like the first Sonic the Hedgehog game, the earliest betas which show the most significant changes have yet to be found, though some unused data has been salvaged from within the released version.
Survivor: Day One (N64)
Most people barely remember this cancelled Konami third person action game. A prototype exists but it was caught in development hell and then axed.
Freak Boy (N64)
A quirky platformer ala Tonic Trouble that was previewed in the early days of NP.