Most rare games are considered as such due to their limited supply. However, there are some distortions like the collector market and distribution region.
The supply, demand and price of Neo Geo really has three phases:
"The Future is Now" 1990-1994
After the first batch of games it was pretty apparent that the Neo Geo was no Super Grafx. The Neo Geo peaked with Fatal Fury Special and Samurai Spirits II (more than likly about 1 was produced for every system I think...just my theory of course).
"The Future is CD" 1995-1999
SNK shifts much of its efforts in the direction of CD gaming, hence the cartrige format is scaled back and released in limited quantities--possibly as a way to absorb excess MVS stock. However, the series fighters are still quite popular: KOFs, Fatal Furys, et al. and are still released in sizable quantities.
"The Future is Nostalgia" 2000-Present
SNK drops support for the CD format. 2d gaming has a dramatcially scaled back presence in the home console format, resulting in nostalgia for the past. People who wanted a Neo Geo back when "The Future Is Now" now have jobs. Games are still produced in limited supplies, but demand has increased. The casual gamers who bought the system and games (AOF 2, FFSP, SSII, etc.) when it was the hot item are now liquidating causing the availability for the common Neo Geo games to increase, and result in lower prices. Many the hard core gamers who intensly collected the Neo Geo games released throughout the "Future Is CD" period are keeping the games in their collections and distorting the availablility of these titles from uncommon to rare or very rare (i.e. Magical Drop 2, Overtop, Quiz Chibi).
Carlson