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danilochka
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Weigh My Fish
I've been researching this for about 3 years now and the number of unique boxes all depends to what level of detail you wish to get into. Often Nintendo would change the games advertised on the back of the box and I class these as different editions of the same variant.

It's probably best to seperate the list into a few more different regions to get a firmer grasp on things. Here's what I've come across so far, although I'm sure it's not going to be everything. Let's start with North American releases:

USA

  • Nintendo 64 [Original]
    // 2 Editions
  • Super Mario 64 Players Guide Bundle [Wal*Mart]
  • Limited Edition Gold Controller Bundle [Toys R Us]
    // 2 Editions
  • Limited Edition Extreme Green Controller Bundle [Toys R Us]
  • Bonus Bucks Promo
  • Atomic Purple Controller Bundle
    // 4 Editions
  • Star Wars Episode I: Racer Limited Edition Set
  • Donkey Kong 64 Set
  • Funtastic Series: Fire
    // 2 Editions
  • Funtastic Series: Grape
    // 2 Editions
  • Funtastic Series: Ice
    // 2 Editions
  • Funtastic Series: Jungle
    // 2 Editions
  • Funtastic Series: Smoke
    // 2 Editions
  • Funtastic Series: Watermelon
    // 2 Editions
  • Pokémon Stadium Battle Set
    // 3 Editions
  • Pikachu Nintendo 64
  • Pikachu Nintendo 64 Set [Toys R Us]
  • Limited Edition Gold Control Deck [Toys R Us]


Canada

  • Nintendo 64 [Original]
    // 3 Editions
  • Violet Atomique Bundle
    // 3 Editions, 4th one probably exists
  • Donkey Kong 64 Set
  • Une Série Funtastique: Fire
    // 1 Edition, 2nd unconfirmed
  • Une Série Funtastique: Raisin
    // 1 Edition, 2nd unconfirmed
  • Une Série Funtastique: Ice
    // 1 Edition, 2nd unconfirmed
  • Une Série Funtastique: Jungle
    // 1 Edition, 2nd unconfirmed
  • Une Série Funtastique: Jungle - Donkey Kong 64 & Expansion Pak Bundle
  • Une Série Funtastique: Fumée
    // 2 Editions
  • Une Série Funtastique: Pastèque
    // 1 Edition, 2nd unconfirmed


Finishing off the NTSC boxes with the Japanese releases, I've included the 64DDs for completeness:

Japan

  • Nintendo 64 [Original]
    // 2 Editions
  • Pokémon Cards Bundle
  • All Nippon Airways [ANA]
    // 2nd edition original box with unique console
  • Official Ticket Station Lawson [Competition]
    // 2nd edition original box with unique console & controller
  • Gold Model [Toys R Us]
  • Orange & Black [Daiei Hawks]
  • Clear Black
  • Midnight Blue [Toys R Us]
  • Clear Grey [Jusco 30th Anniversary]
  • Clear Blue
  • Clear Red
  • Pikachu Orange & Yellow
  • Pikachu Blue & Yellow
  • Nintendo 64DD - Randnet Starter Kit
  • Nintendo 64DD - Retail Version


Now for the PAL Stuff, it's easier to first list all the boxes unique to a particular country, then lump everything into a general Europe category. All Australian consoles boxes were unique to them:

UK

  • Nintendo 64 [Original]
    // 4 Editions
  • Limited Edition Gold Controller Bundle
  • Limited Edition Gold Controller + GoldenEye 007 Bundle
  • Super Mario 64 Bundle
  • GoldenEye 007 Bundle
  • Star Wars Episode I: Racer - Limited Edition Set
    // UKV Edition
  • Banjo-Kazooie Bundle
  • F-1 World Grand Prix II Bundle
  • Pokémon Stadium Battle Set
    // 2 Editions; with and without Pokémon: I Choose You Pikachu! VHS


France

  • Le Pack F-1 World Grand Prix
  • International Superstar Soccer 64 Bundle
  • International Superstar Soccer 64 + Super Mario 64 Bundle


Germany

  • Nintendo 64 [Original]
    // german only
  • Pokémon: Pikachu Nintendo 64 + Super Mario 64


Spain

  • Nintendo 64 [Original]
    // 5 Editions
  • Mario Pak Soccer


Italy

  • Nintendo 64 [Original]
    // 2 Editions


Scandinavia

  • Nintendo 64 [Original]
    // Bergsala AB Edition
  • Super Mario 64 Bundle
  • GoldenEye 007 - Special Value Pak
  • Mario Kart 64 - Special Value Pak
  • NHL 99 - Special Value Pak
  • Zelda Special Value Pak
  • 1080° Snowboarding - Special Value Pak
  • Donkey Kong 64 Pak + Super Mario 64
  • Pokémon Stadium Battle Set
    // 7 Editions possible
  • Perfect Dark Bundle
    // 7 Editions possible


Belgium

  • I Love Techno Value Pack
  • The Legend of Zelda: Ocarina of Time - Limited Club Offer


Europe

  • Nintendo 64 [Original]
    // German & French
  • Nintendo 64 [Original]
    // French & Dutch
  • Nintendo 64 [Original]
    // German, French, Dutch & Spanish
  • Mario Pak [Punching]
    // 2 Editions; 1 German, 1 French
  • Mario Pak [Grey]
    // 6 Editions; localized price stcikers
  • Star Wars Episode I: Racer - Limited Edition Set
    // EUR Edition
  • Color Edition: Atomic Purple
  • Color Edition: Fire Red
  • Color Edition: Jungle Green
  • Color Edition: Ocean Blue
  • Color Edition: Smoke Black
  • Color Edition: Sun Orange
  • Noir Slipcover
  • Donkey Kong 64 Pak
  • Pokémon: Pikachu Nintendo 64
  • Pokémon Snap Pak
    // French & German
  • Clear Blue + Super Mario 64
    // 2 Editions


Australia

  • Nintendo 64 [Original]
    // 4 Editions
  • Limited Edition Gold Controller
  • Twin Controller Pack
  • Fire - Red Panel Version
  • Grape - Red Panel Version
  • Ice - Red Panel Version
  • Jungle - Red Panel Version
  • Star Wars Episode I: Racer - Limited Edition Set
  • DK64 Crate Bundle [Competition]
  • Special Limited Edition Pokémon PokéManiac N64
    // 2 Editions
  • Charcoal - Biggest Names In Games Version
  • Fire - Biggest Names In Games Version
  • Grape - Biggest Names In Games Version
  • N64 Stars / Spotlights Slipcover


Not forgetting the rest of the world:

Brazil

  • Nintendo 64
    // 2 Editions
  • Super Mario 64 Bundle
  • Atomic Purple Controller Bundle
    // contains 1 grey plus extra 1 atomic purple controller
  • Edição Especial Nintendo Futebol
  • Edição Especial Nintendo Futebol 98
  • Série Multi-Sabores: Anis
  • Série Multi-Sabores: Cereja
    // Unconfirmed
  • Série Multi-Sabores: Jaboticaba
  • Série Multi-Sabores: Kiwi
    // Unconfirmed
  • Série Multi-Sabores: Tangerina
  • Série Multi-Sabores: Uva
    // 2 Editions
  • Edição Especial! Atomic Purple
    // 2 Editions


Asia

  • Nintendo 64 [Original]
    // Hong Kong version
  • Nintendo 64 [Original]
    // Unknown Asian version
  • Hyundai Comboy 64
    // South Korean version
  • iQue
    // China
  • iQue Family Package
    // China


And that's all I know, well excluding micro-variants at least. If you have any questions about any of this just ask.
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