There are many ways to set this up. The most common is to use 2 DVI ports and either the HDMI or Displayport ports. If you need to, you can get an adapter to convert HDMI or Displayport to DVI, so that you only need monitors with DVI inputs.
Personally, I use a Club 3D MST hub (model CSV-5300) connected to the Displayport plug on my GTX 680 and run 3 Displayport cables to my monitors (1 per monitor, of course).