A while ago, when Mupen64 was (dare I say it) a hassle to use, I used Sixtyforce for everything. I still use it for some games that I don't mind not having saves. To answer your question, practically every one of my N64 roms worked. If they don't run too smoothly, play around with the settings: set the texture cache to 32, uncheck "Dithered Alpha", etc.
Personally, I love Sixtyforce but am too cheap to buy a license. Hence, I use Mupen64Plus. Love it, but if you either cannot use the Terminal or don't have an interface externally (I wrote mine ), it's a hassle.
You know, I understand there's difficulty in learning programming and trying to reproduce hardware functionality on a completely different system accurately. But I never supported the idea of paying for something like a game console save function, it's like paying for the whole emulator basically.
The whole idea behind using an emulator (originally, anyway) is to be able to play the games you own on your computer, which gives some added advantages the original consoles don't, especially on laptops. Having to pay for "the console" again is not really worth it in my opinion, especially when it's not even as accurate as the real thing. Add to that, the fact that there exist more accurate and updated emulators available with more functionality, available info, and compatibility, completely free, it seems like it adds insult to injury.
Using the shell for Mupen64Plus is definitely not hard in the slightest. It may be a tad confusing for the typical end-user not familiar with shell usage, but there's an abundance of documentation and help available that answers almost all of the basic questions (such as "how do I configure my buttons?"). Besides, there's also the GUI front-end that SpeedofMac released. Anyone who can't figure that out might want to forget playing games for the time being.
Open source software with high development activity (or even moderate) tend to wind up better than most of the alternatives, anyway.