I'm knee-deep in a personal project that involves reverse-engineering a USB device; since the only drivers for the device are for Windows, the solution was to virtualize Windows on a Linux host (presenting the USB device to the guest OS), fire up wireshark on the host OS (using the usbmon kernel module), interact with the Windows software and drivers as per usual, and capture anything the guest OS sends to the device for analysis.

Really simple stuff; much easier than following this stuff with scopes or logic analyzers.