First of all, video games are a horrible long-term investment. So if that's your intent I would look for something else.
But to answer your question, big name titles (mario, zelda, sonic, etc...) will always sell slightly higher than the average simply because of name recognition.
Otherwise there's not any way to really tell when a game will be worth more or not. Limited releases and/or collectors editions will usually be worth a little more, but not always (halo 2 collectors edition for example, only sells for a few dollars more).
One of the biggest factors towards value will be pop culture, earthbound is a perfect example of this. It's not rare, it wasn't a smash hit when released, and for a long time was pretty much worthless, until a few years ago when its name suddenly started circulating around the internet.
Firepower 2000 is another great example, it rose over $20 in value when the AVGN did a video about it, and still hasn't quite stabilized. But thats just about the only thing that could ever make it worth more than a few bucks. Once again, its not rare, wasn't super popular, and didn't cost too much.
Also, hidden gems are usually not worth a lot.
Just go on ebay and look at "completed listings" to see what a game usually goes for right now, thats really the best judgement of something's [online] value.