How to Use 3 Monitors

I'm just migrating to a 3 monitor setup myself. Basically as long as the graphics card works, you can use it. I'm geting 2 Nvidia 8600 PCI-e cards and I'm not using SLI (Motherboard doesn't support it), however SLI is not required.

Almost all operating systems I know of support multiple monitors, as long as the gfx card is enabled, then you can use it.

As for built-in VGA ports, there's no reason that wouldn't work either, though I think most BIOSs disable the on-board display if they detect you've got a gfx card, so you may have to change the BIOS setting so that the onboard VGA is initialised.

Edit: As Will points out, Vista is a bit picky when it comes to multiple cards, all the cards need to use the same driver, so you won't be able to use onboard and another gfx card under Vista.

I would use a second computer and connect the two computers with synergy. Synergy is a software based kvm switch, so it feels like you are using one computer. It's great if like running linux, but you still need a few windows apps. You can keep the windows stuff on the computer with one monitor and have your linux box run the two other monitors. It works on mac too.

An interesting option if you can't add an additional graphics card is to use a USB video card: http://www.evga.com/products/prodlist.asp?switch=10

Jeff Atwood recently detailed this in his coding horror blog and listed gfx cards with 3 outputs.