While Nestopia is not as loaded as other console emulators (ZSNES, for one) it still does its job respectfully. When you first open it, it will prompt you to load a ROM (either the most recently loaded ROM or one from a certain folder). Once the ROM is loaded you will have a few simple options. You can increase the size of the window to full screen (which is recommended since the Nestopia window is hardly bigger than the average internet avatar). You can also take a screen shot or freeze a game state easily by clicking on the Options menu. Within Nestopia freeze states are really the only way to save games since most NES game didn't come with save points to began with.
There is also a useful preference menu within which you can configure the video, speed of emulation and other advanced options. In addition, you can configure your keyboard with the keys you want to use while you play ROMs.
One of the largest downsides of Nestopia is the lack of controller support. You can purchase Emulator Enhancer for USB controller support, but it costs $30 and I'm too cheap to buy it. Also, this emulator takes a minimum of 600 MHz to run. Not that this should be a problem for most modern Macs, but it may pose a problem for older ones.