Have a look at the Saleae logic analysers for example, they combine an FPGA with an EZ-USB FX3, in the case of the Logic Pro 8.

http://www.eevblog.com/forum/testgear/saleae-logic-pro-8-qui...

I believe the FPGA is often being used for converting fewer high speed inputs, to a greater number of lower speed outputs for the GPIO of the FX3, I think that's called SerDes (please correct me if I'm using that phrase incorrectly).