There are numerous ways to go about setting up a computer audio system and probably far more qualified people to explain the ins and outs but I'll try to give some basics.
Option 1:
Get a decent soundcard like an EMU 0404, output to your headphone amp of choice.
Option 2:
Find a decent bit perfect soundcard for a reasonable price, the Chaintech AV710 comes to mind, use the digital output to an external DAC then to an amp.
Option 3:
There are a few combination DAC/amp products on the market now like the new Meier Audio Aria which has a USB DAC and what is supposed to be a very good amp for a relatively reasonable price.
Option 4:
Output to a Squeezebox then to a DAC and/or amp.