Yes there is no problems having a second Video card in your PC , I been running 2 Video Cards in my system for years with out any problems , it works in 98Se and XP . It's very handy to have 2 or even 3 monitors when I'm doing some work in PSP or Flash . you can have several files and programs open at the same time and see them all. just the other day my PCI Video card died ( Of natural causes ) wile I was doing some work in PSP. I remembered I still had a old PCI 4 Mb Viper 330 in my drawer so I put it in and worked just fine.
As Dee-ehn said sometimes there can be a few problems running 2 cards,but it's not very common. The best way I found to do it is to put your PCI card 2 or 3 PCI slots down from your AGP card , sometimes they interfere with each other , one other thing to remember if you put a PCI video card in , by default your mother board will use the PCI card as your main Video card and the AGP card as your second Video card, if you want to play some games it will try and play it on the monitor that is connected to your PCI card, in that case all you will have to do is go into your Bios and change the default settings so AGP is your main card and you shouldn't have any problems.