I personally like using Project64 and DeSmuME in Wine since Project64 is a well supported emulator and DeSmuME has more feature on Windows than it does with its native linux application. It would be cool to see runners that support emulators within wine and be able to select the Wine Prefix just like the Wine runners can.
This way it will be easy to add a Windows emulator game into Lutris, all you need to do is give the game a name, select the wine prefix, exe file and the ISO file directory.