Communication with NIOS2 over USB

I don't know of any standard Comm applications that speak with the talk with the JTAG UART in the nios processor except the Nios Console app. (I may be wrong)

I would just tap on a simple usb-serial baord like this one:

http://www.sparkfun.com/products/718

This gives your computer a standard usb-serial converter and only requires a few wires to hook it up to some GPIO's available on your board.

This way it also looks like a standard USB Serial port on your computer.

Pete