For games that had low prints like Xenoblade (Wii) and Twilight Princess (NGC) it's understandable that their price has arisen but then you've got Super Smash Bros. for the Nintendo 64 (the 3DS/Wii U are called exactly the same minus the last part -- platform). still holds its price very well even if it's only the cartridge the price continues to be up on the £30's and more (it's ridiculous).
Now when it comes to PlayStation and Xbox exclusives, their prices are completely different the games are below £10 (or even £3-5) which is really cheap whereas for Nintendo you've got to fork out sometimes between £20-30.
I believe that if a game is of high quality, then whatever its price is then it's worth it (I paid £32 for Twilight Princess and I could've bought a new gen game instead), as long as it's not overpriced (scalpers tend to do it a lot).
Ah yes, Dreamcast games seem to be rising too but I think I'm done with it since I've got the ones I wanted, there are a few I'm missing out but eh, not gonna spend too much on those (Shenmue 1 + 2).
Demand. It's as simple as that. Nintendo is a company that mostly targets kids. Kids have no buying power. By the time they are adults and have an income of their own, some yearn to play the games of their youth, which means they're willing to spend higher prices. All it takes is for one seller to price a Smash Bros. N64 cart at $50 for then another one to see it and do the same. Soon all sellers sell it for that, and then the price goes up and up.
Ah yes, it's the demand for it.
As much hate as Wii U's getting since 2012 since now its games will increase in value within a couple years, more so the exclusives and certain multiplatforms (which had low prints, i.e, Most Wanted, Sniper Elite V2, etc).