With the V3-2k you prolly won't notice any difference between the pci and agp (maybe a few stats, but prolly nothing you'd actually see). The V3-3k in agp only.
As for TNT or V3, depends what kind of processor you have. Generally if you have faster, tnt will work well. If not then go V3. V3 still has better support for AMD right now, but nvida is supposed to come out with 3d-now supported drivers soon.
As for better? don't buy till you try is my motto (or at least buy them both and return the one you didn't like If you decide to go V3 - get the V3-3k(which is agp only), get the o/c util, and you'll have a V3-3500 for a lot less. V3-2k about $100, V3-3k about $130.
As for pci v. agp - as I said, w/v3 you prolly won't notice, but going agp frees up a pci slot that can be used by something else...
I call it "No-Pants Wonderday," but it turns out the police just call it "Thursday." Go figure.