RetroArch Stable builds is a All-In-One solution for emulators. It's more advanced to setup compared to running standalone counterparts, but the pay off is worth it.
Current stable build is 1.2.2, one you download and extract it you simply run RetroArch.exe. The default interface is similar to the PS3. X is confirm, Z is cancel.
You can remap virtually any controller, and keyboard key to whatever you want under SETTINGS > INPUT USER 1 BINDS.
Downloading CORES is the actual emulator itself, just go under Online Updater > Core Updater, and download the emulators you want from here. For N64 I would recommend Mupen64Plus, and for SNES get bsnes Accuracy, Balanced or Performance depending on how on your computer hardware.
> NOTE: The standalone version of bsnes is officially called Higan now, but RetroArch still refers to it by bsnes. Higan, however, can actually emulate several Nintendo emulators itself. If you don't want to learn how to setup RetroArch I would recommend checking out the developers website http://byuu.org/emulation/higan/
> NOTE 2: Mupen64Plus is hosted on GitHub now, their home website is http://www.mupen64plus.org/
I played occarina and majora's mask to completion. Here's a compatibility list that should give you some good previews of how well stuff should work.
It's a command-line application, not a command-shell. It expects you to run it from the command-line so you can type in parameters and arguments (like what file you're trying to play, the resolution, and what plugins to use). If you just click on it, Windows will try to run the program via the command-line, but it quits because Windows never gave it any parameters or arguments. A lot of command-line programs quit like that.
In Windows 7 and up, there is an option to open the command-line from the current folder (you do this via Explorer). If you do that, you can type in something like this:
>mupen64plus-ui-console.exe --resolution 800x600 C:\Games\N64\FavoriteGame.n64
Then hit Enter. There are a lot of other parameters and arguments you can pass to Mupen64Plus. Have a look here -> http://www.mupen64plus.org/wiki/index.php?title=UIConsoleUsage
If you'd prefer something with a GUI, look up M64Py -> http://m64py.sourceforge.net/ or RetroArch.