Yes it can work with 1 AGP and 1 PCI card, although whether it'll work with 1 PCI-e and 1 AGP i'm not 100% sure of. To get all monitors working it's best to get the same brand graphics card, in the above i'm using 2x 7800 GeForce Ultra Extremes, with 4 DVI outputs in total.
If you dont fancy having 2 graphic card, you can always get a matrox video card, they have 3 outputs on 1 card, but I think you need a PCI-e board.