Sure - but that doesn't mean they were actually sound investments. Investments that you could, you know, stake your financial well being on.
The trick is to convince other people that the given item is, well,
that important. And it only becomes easier because people had/have great memories with games. People looking to relive those experiences tend to congregate, and markets pop up to cater to that impulse.
Then you've got people so see this and think "I have a copy of Metal Slug I want to sell, and I've found a community of buyers that will willingly pay 1000 (or whatever price it goes for these days) for it." They find their mark and sell it. Then they think "Hey - maybe I can do this again. Gotta find MS and other 'rare' games." Over time, at least in a collector's sense, the pursuit becomes one of profit first and foremost. I'd wager that's how many collectors come to see their games as "investments."
What's worse is that places like eBay and the N-G.com market forums are so great at perpetuating that message: they concentrate and amplify an arguably false sense rarity that falsely implies high value. And as long as there are nostalgic doe-eyed people with cash to burn who accept that the legitimate price for a copy of Metal Slug is 1K, the idea gets affirmed through transaction after transaction. This only further reinforces the idea of an "investment."
If you're of a particular mindset, you might think that this kind of kills the innocent 'spirit' of simply enjoying a game at a(n arguably) fair price. That is, playing a game for the sole sake of playing with no overwhelming desire to flip it for a profit. Digital downloads come with DRM and the like, but at least you can argue that they're expedient and affordable.
Can't say I know where to go from here, but being able to play a given game when you want to, cheaply and in the least burdensome way, is a good thing.