It's easier to just find complete sets, rather than trying to download individual roms. Underground Gamer is where I used to always get all of my ROMsets, but they are of course long gone. Pleasuredome is an alright site, but it seems like it's down too. The Internet Archive has listings for ROM and image sets, but they go up and down.
Underground Gamer was the best. I use to spend hours upon hours in that place trying to upload stuff so I could download entire sets. There was another one similar to that site that shut down to, which was almost as good. Can't remember the name though. Emuasylum, also use to be solid. For all my music, I really liked Oinks Pink Palace. That was a top-notch site, with only CD quality stuff.
Anyways, this has been long coming. Between emulators and everdrives, anyone on this website should have had a set of every cartridge based system since like 2003.
There's so many rom sites anyway that Nintendo will never be able to kill them all. It would be in their best interest if they realized that these places are the only real places that actually care about archiving these old games. If they would just release a "mini" console, with a built in virtual console, dedicated to bringing all these games back... then they could probably cut down on this piracy a lot and actually make some money.
I think once you get into ISO's, that's the point where you really need to make an educated guess to determine if you're actually ever going to play the game.
Do you really need 3 gigs of Mary Kate and Ashley Olsen shit taking up space on your HDD?