Ah, but this is the key: "Especially if you were there at the time and have fond memories of it yourself."
The Japanese versions of Nintendo games don't hold any emotional significance for most people - it doesn't take them back to their single-digit-year-old self, standing in the aisle of their department or toy store, gazing longingly at the items and wishing you could take them home and play them. People are trying to recapture a feeling from their now-distant past - and they're willing to pay handsomely to have their heartstrings pulled that way. And, because these games were widely popular, there are a lot of people competing for that feeling.
It can't possibly be rational, these prices - it's emotional and irrational.