Neogaf's Sixtyfortyfive has found out something really fascinating about Virtual Console and its inner workings today. Like everyone else, he was thinking that virtual console games are untouched rom files.
This was until certain obsessed fan wanted to fully complete Phantasy Star IV and get every character up to level 99. As most diehard Phantasy Star fans know, this actually launches bug in the original game, with stats going berserk, and characters starting to forget their abilities. But in the VC-version this bug has been fixed!
Sixtyfortyfive was so interested about this that he started to do some hexediting to Phantasy Star IV's VC-channel. What he found out was interesting.The rom file inside the channel is literally same as you can find from original cartridges. The channel, however, applies simple patch over the game when it is booted. Depending on which version of rom is run, this patch fixes various bugs, like some minor graphical glitches on japanese version, and aformentioned bug when someone hits 99th level. There is also commented (meaning that it won't be run) patch that allows player to get experience much faster. It was probably used to test lvl 99 bug.
The significance of this is pretty big. It means that Nintendo isn't just dumping rom files out, but actually debugging and bug fixing games before release. Which probably explains the slow speed with the releases. It also means that Nintendo could relatively easily put 50hz/60hz switch on the games, or sell expansions to its old games.