[T. Payton] "So what is the difference between the .mov and the .mxf (besides of course the extension)?"
MXF is a container, like .mov. It can house all kinds of frame rates/sizes and codecs, most of which can be proprietary codecs like ProRes or AVC-Intra.
It stands for Material eXchange Format. It was quite literally designed to hold and exchange modern file based media by SMPTE.
The MXF container itself is open, which means you aren't bound by any one developer or manufacturer provided you also have an open codec. MXF is used extensively in broadcast post/archive workflows, many modern broadcast tapeless cameras shoot to an MXF wrapper.
It is platform agnostic and makes sense for modern file based workflows. QuickTime is dying, not so much the container, but the API behind it. This means that NLEs will be restricted to decoding .mov material in an old and creaky 32bit structure. MXF skirts this as it's a more modern architecture, and also has cool capabilities such as built in metadata structures.
For all of its faults, QuickTime has been ubiquitous and user friendly, I feel that should change for a few reasons and hopefully MXF should get better attention.
MXF is not perfect, but the more that it catches on in post workflows, the more development resources can be thrown at it. Avid uses MXF as its underlying media container, but avid does it's best to over complicate it and hide those underpinnings from the user as much as possible.
I am curious to see what happens with FCPX and MXF and the MacOS in general. With Mountain Lion, AVCHD Transport Stream file structures are now directly available to the OS for viewing. It'd be cool if we could get this same functionality with MXF files.
Wikipedia has good info and this is a good read if you like this sort of thing:
http://tech.ebu.ch/docs/techreview/trev_291-devlin.pdf
Jeremy