Think Project64. For linux. That’s what Mupen is. I’d debate that Mupen even works better than Project64 in some cases. I found this in my search for a Nintendo 64 emulator for linux, since Project64 doesn’t work (well, not native at least). Plopped some games I had in it, and it mostly worked. After about 15 minutes of fooling around with the settings I got it to be fully functional.
When it starts up it has a clean interface of all the games you have on it, and then you simply double click the game and it starts up. For the Gfx plugin, i use glN64, and for Input I use blight’s SDL input. Other than that I pretty much left the settings alone.
I’d have to say this is probably one of my favorite emulators of all time. You can get it at http://mupen64.emulation64.com/
Here’s a screenshot from their website: