Recently I was contacted by someone claiming to be a researcher for a TV program, and they were interested in my opinion (as a somewhat disreputable seller of pre-abused crap) of the rarest game ever. Here's my response:
Hi <name deleted>.
While I don't have these games in stock, the rarest games are not really well known, if you ask ten people you'll probably get ten answers. This is the problem with rare things - not everyone's heard of them, and what's rare is almost by definition unknown.
Then there's the matter of definition; are we counting only commercial releases? No fan-made games or unreleased softs, but what about promotional titles, like the Gran Turismo promo recently released through Toyota dealers? Japanese gamers are used to special promotional games, like the special version of Magical Drop 2*, featuring DJs from a Tokyo radio station, that regularly sells for over $600 in Japan.
Rare games are going to be most often tied to rare consoles; anything made for the Halcyon is going to be absurdly rare; nothing released for the SuperNES can even compare.
What's rare one day can become suddenly common the next; a PC Engine game called Circus Lido was in feverish demand, a friend of mine paid over seven hundred dollars for a new copy, only to find Amazon in Japan had 120 of them in stock for $40. Someone somewhere found a warehouse shelf of the things and the value, and rarity, was suddenly very different.
I was recently unfortunate enough to be involved in a conversation where the top-10 rarest game consoles were being decided, and things like the Taiwanese Super A'Can was on the list even though an electronics surplus/wholesaler** was dumping them at $2 each at one point. Presumably the system's more common in Taiwan, but no one involved in the discussion know anyone in Taiwan who could verify.
Edge magazine has recently run a series of retro articles discussing rare games for the MegaDrive, PC Engine and Saturn, but they relied on resellers and collectors, both of which have a vested interest in maintaining high values in their games.
The only way to get accurate reflections of a game's rarity is to get production numbers from the manufacturer, and they're notoriously reluctant to give that information out.
All that said, since most games receive print runs in the tens of thousands, there's not really any game that can be considered rare, they're just more sought after than others at any particular time. The rarest game I've had in stock recently was Sapphire for the PC Engine, and it's not really rare, just expensive. $400 is about the least you can expect to pay. I've got some Tokyo Game Show promotional cartridges made by Compile to show off an unreleased game, complete with a playable level and show-only title screens, but this wasn't released - does it count?
The kind of answer you're looking for I imagine isn't the one I've got. Rarity is a subjective matter in the absence of hard facts and, sadly, there are no facts, just opinions and observations.
That said if you need anyone to debunk someone else's opinions I'd be happy to offer my opinions on other peoples' lists.
Thanks for asking,
* Should have mentioned this is a SNES title.
** Should have mentioned this is a US company.
Also should have mentioned the neo carts like Chibi Maruko Quiz (or whatever it's called).