It shouldn't be a problem with any new cards that come out, even if they are a different brand. I remember reading on some review site that they had 4 monitors on one computer using one dual output ATi and one dual output nVidia.
A couple years ago I tried to setup a second display using an old PCI tv-tuner card. It wouldn't work with AGP card for some reason or another. If I disabled AGP it would work fine. The TV tuner was from an old Gateway Destination made in 1998 though. =P