If you are talking about a voodoo2 card, there is no performance increase getting the agp version over the pci version, as the voodoo2 chipset is a pci chipset. The agp versions of the card have only one thing in common with agp, and that is just the slot. It is built on pci archetecture, just modified to run in an agp slot, and it does not use any of the bandwidth of the agp bus. Another draw back of the agp voodoo2 cards is that they are not sli capable. You will be stuck with one card. Your best bet (if you want a good 2d card, and a seperate 3d card) is to get a fast 2d/3d combo card for the agp port (such as an i740 card, or a riva card) and add a pci voodoo2 card. That way you are getting the best of both worlds, and you can add a second voodoo2 card in the future if you want to run really high resolutions with killer frame rates.
Ps. Your true best bet and buy would be to not get a 3d add on card at all, and just get a really fast agp 2d/3d card such as the riva tnt, and save yourself some deneiro.
And if you do decide to go with a 2d AGP and an add-on PCI. Get a board based on the 1740 chipset for your 2d. The 3d is mediocre at best, but has excellent 2d resolution and color, and is cheap. I've see nthe Hercules Terminator? 1740 for as low as $80.00
Or get a Canopus Riva 128, It has witchdoctor technology, a reverse pass through for plugging your voodoo1 or 2 intro the riva, to get much better output quality