I discovered that there's a trojan in the "updated" Project64 installation I got from somebody here, so other people might be using it.
This installation is popular because the version number indicates that it's newer than 1.7.0.54, which is one of the latest (if not the latest) build released by the emulator team.
The infected file is:
NRage-Language-1034.dll
Some info on it:
http://securityresponse.symantec.com/avcenter/cgi-bin/virauto.cgi?vid=25464From what I've read since getting that installation, I've read that it's the exact same as Project64_1.7.0.54 but with some updated plugins. I'm gonna see if that's true.
One thing which should've tipped me off was the installer, and another was the mix of languages inside the menus, which isn't normal for that software.