Believe me, there will be some idiots that will go for gamecube WRs, I guarantee it no matter how lowly gc is looked down upon.
The point is that, even if this happens, nobody will care about the record. So if there are people that go for gamecube records because they care about it for whatever reason, then good for them. And if the Gamecube version does gain popularity and competition, then that just means it deserves the record would be more meaningful to more people. I don't really see how this is a bad thing. Although I don't expect that to happen.
Here's my idea. Have 2 LBs, 1 for official verified runs and one for all runs. On the first one, all the times that are present will be all the n64, gc, vc and ique time that have a video and that have been verified, and on the other, have all times, any system, video or not. This way, people will see the "official" leaderboards, but emu runners won't be completely shut out and their times will still appear and can be verified by admins. Same deal with people without any means to capture their game, their times can still appear on LB #2
This sounds pretty much like the compromise Cosmo suggested, except still allowing emulator runs to be verified. I kinda like this, simply because I recognize that if you don't verify emu runs, then there is no incentive for them to be checked thoroughly. I'd hope they would be checked anyway, but maybe this is a better idea. Basically have a tag for "verified" and another for "official".