Gizmodo recently posted this video, which is beautiful to any PSX-era gamers: it's Final Fantasy VII running right on the iPhone, like buttah thanks to the 3GS hardware. How is this possible? Through the magic of emulation -- ever since computers got powerful enough to pretend to be other computers, people have resurrected old consoles and hardware by writing code that makes old games and software think its right at home in the computer it belongs in (an old NES system, a Genesis, or even a Playstation or Nintendo 64). As a result, by loading up ROMs into an emulator program, you can play old games you can't find (at least working) in the store any more.
But the problem, as it usually does, lies in the legality. Even though those games are hard to find, companies still often own the copyrights on them (Square, for example, just released FFVII in an official emulator on the PSP, and they wouldn't be very happy with someone else releasing it on the iPhone). So while it's very easy for someone to write software that pretends to be an old NES (and there are lots of jailbroken apps around that will do just that), it's not easy to get all the rights and legal sign-offs to make it legit. Legit enough for Apple to keep it in the App Store, anyway. And while the video Gizmodo shows is awesome, and is possible on a jailbroken phone, it's not likely we'll ever see that app make it through Apple's approval. Not to mention that even when people jump through the legal hoops, Apple isn't happy with running other systems' code on their hardware anyway. Lame.
That doesn't mean that the old games are gone forever -- there are certainly emulators of open-sourced or expired hardware on the App Store (here's one for Chip-8), and obviously there's a commercial reason for companies who do own the copyrights on popular games to bring them into the App Store officially. But as great as it would be to have a GBA emulator that automatically played any GBA game ROMs you loaded into it, that kind of stuff will have to stay in the jailbreak underground for now.