MR-HD100 16x9?
 

How do I get my MR-HD100 to record 16x9 in DV mode? The files say they're 720x480 but when I import them they're 4x3.

That totally depends on the settings in your camera, as the Firewire drive is just recording what comes out of the camera. The MR-HD100 does no conversions internally.
Check for anamorphic settings in the 16:9 modes in the camera.
The best is to use a setting where the camera is recording the 16:9 without black bands, and to set the setting in your NLE. This way you record the most pixels on harddisk, as the black bands are lost pixels.
Especially when you need to pan and zoom, this extra available pixelinfo will give you better results.