Fit is a command-line tool that works with any HTML document. It specifically works with Word documents (saved as HTML) and you should be able to use any other HTML tool to create your Fit documents as well. You can import from Excel by using cut-and-paste.
FitNesse is a Wiki that includes a modified version of Fit. It's designed to be an integrated tool. You use Wiki syntax to write your documents. You can import from Excel with FitNesse, too.
Overall, I would say that FitNesse is easier to get started with and Fit is more pliable. For example, FitNesse includes revision control out of the box and with Fit you have to set up your own--but with Fit you can use your existing revision control system and with FitNesse you can't.
I also think that Fit is friendlier to business types, whom I've found to be more comfortable working in Word than Wiki. I'm biased, though. :)
We'll be releasing Fit v1.1 later this month. A major focus of that release is improved documentation at http://fit.c2.com. You can see the beginnings of the new documentation there already.
Fit project coordinator