Well, "rarity" can often be a relative term, and for the most part rarity is determined by supply vs. demand. Many titles that are considered rare are often expensive because the supply (no matter how small or large it really is) does not meet the demand. In some cases, titles may be more "rare" for certain systems simply becuse of increased demand for a copy on a certain console. Other times, there is simply a smaller production run of a game on certain consoles.
For instance, the production runs for most titles released for Intellivision and ColecoVision are much smaller than their Atari 2600 counterparts. There are several reasons for this, one them being the fact that there were several million more 2600 systems owned by gamers than either INTV or CV. Another reason for the shortprints of INTV/CV games is the fact that many companies were slow to produce games for these systems and by the time they did, the market was beginning to crash (1983-84) and this halted production.
A good example to demonstate this is a game like River Raid by Activision. The game was first released for the Atari 2600 in 1982 and was a huge hit. These are very common. When Activision decided to release games for ColecoVision in 1983, River Raid was one of the first titles they released for the system (along with Pitfall). CV copies are nowhere near as abundant as 2600 copies but fairly common in CV terms. Activision also decided to release games for the Intellivision in 1983, but they were late in entering the INTV market and they only ended up releasing 7 games for the system. Of these, the first few titles (Stampede, Pitfall & Happy Trails) are very common. When the market started to crash, the production runs on subsequent releases (Dreadnaught Factor, Beamrider, Worm Whomper) went way down. For some reason, they held off on releasing River Raid. In fact, it was the last game they released for the system and the production run was very, very small. Consequently, a complete INTV River Raid is worth over $100.