For goodness sake, don't let TSS see this post! Just kidding, Rick.
There are a lot of reasons for a game becoming rare (as in seldom found), and not all good. But a couple big reasons are that it wasn't distributed in the U.S., it got pulled from the shelves almost right away for company problems or whatever reason, or it just didn't appeal at the time with lots of competition.But you'll notice on ebay if one shows up and gets a big price, others will often follow, and you see that the "rare" game is not really hard to find at all, i.e Neverhood.
Off the top of my head, hard to find: Treasure Hunter, Alice-Interactive Museum, Alien Incident, Touche, Jack the Ripper,Blue Heat, Chewy-Escape from F-5 and SFPD homicide.
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"How could drops of water know themselves to be a river? Yet the river flows on."
- Antoine de Saint-Exupéry