When you say 'USB', are you intending to have a full USB stack on the board, so you can be an arbitrary USB endpoint (eg keyboard, mass storage, printer, camera)? Or will something like a USB-serial adaptor work - you talk to what you think is a UART, but it's converted by an additional chip to serial-over-USB.
The latter is much simpler, but imposes restrictions - you only show up as a serial port and you may be limited in speed (1 Mbps or so).
JTAG over USB is slightly different, but often has similar constraints.
Papilio One appears to be USB over serial (FT232).
Do you have a particular preference of FPGA vendor?
Theo