Best bet would be to use a microcontroller with USB support (like Axon or Arduino). Have the microcontroller read the data coming from the N64 controller. Process the data however you like, and output that data in whatever form you want through the USB on the Axon/Arduino.
Now if you mean "making a controller work on a PC" as in emulating a gaming joystick, that would be a lot harder and you will need to purchase the right USB chips to emulate a USB joystick. Basically too much work, this is something a team of EEs would do to develop a real product.