Earthbound is 'rare' in that, compared to the likes of Mario & such, it had a much lower print run. It's not something you can expect to find in every game shop you ever visit. It's got enough reputation as a 'pricey' game, however, that plenty of resellers gobbled up copies and are now looking to turn a profit. Which is why the prices don't seem to drop- these guys will happily sit on those copies for years until they either turn a profit, or it becomes readily apparent they have to lower their prices. Which tends to happen when players/collectors selling amongst themselves drop prices to expedite sales- after all, we want to buy new games more than make a certain amount of money.
I tend to use the Ebay test for true rarity- basically, look up a game and see how many listings there are. If you can find a dozen copies for sale at any given time, it's not really that rare. There's several dozen Earthbounds up once you scroll past the obvious fakes. Then on the flipside, you have something like Video Whizball, an old Channel F game that most people won't have heard of. That one's rare enough that most days, there are zero copies available on Ebay. Most games like that, that are truly rare, have no set value becuase there's no past data to really pull from. In the case of Whizball, in the year I watched Ebay, lamenting listings I missed by minutes, I saw it go as low at $5 and as high as $200. I ultimately paid $40 on a different forum.
It's also worth noting that everyone has different ideas of what a properly 'expensive' game is. I, for example, wouldn't blink an eye at a $20 game, especially one of known quality like a Zelda or Mario. Over $30 is 'pricey', expensive doesn't start until $50, and unaffordable is well into triple digits. Meawhile some people drop $1000 or more on single titles without a concern. Honestly, that's kind of the nice thing about gaming- almost every income level can find something enjoyable for themselves in it.