I'm in the same boat....decent machine with no AGP slot. I've done a ton of research on this, and pretty much come to the conclusion that the v5 5500 pci is still the best option, if you can find it for a reasonable price.
Here's some of the reasoning. The gforce2 mx's (1st generation) are solid performer's in their AGP versions; bandwidth requirements needed for the geforce's more complicated features (T&L, big textures etc.) are just too choked by the PCI bus to see the benefit. The MX200 and MX400 are just castrated versions of the original MX, and are the most common iteration of the PCI Geforce's. They have badly neutered graphics pipelines, and use slower memory that can't really be over-clocked.
Kyro II and Radeon are both solid performers, but they are just too hard to find! I still haven't found a kyro 2 pci that is actually for sale, and I'm pretty sure the v5 beats the Radeon SDR (even if its similar, the FSAA is worth the slight hit). There's the All-in-wonder DDR Radeon, but do you want to spend $200+ on a pci card?
The voodoo 5 pci was identified in most reviews I read as the best PCI card out there, but they didn't directly compare it to other cards b/c of its high price. The cost has dropped considerably in the last few months, to the point you can get one for around $100 bucks. Also, its about the same speed as the AGP version b/c the v5 AGP doesn't fully use the AGP bus. It seems to get the best performance on machines that are PIII 600+, but for lower-end machines, it improves pic quality rather than a drastic improvement in frames. The other graphics chips are even more dependent on the CPU, so you may see even less improvement than the v5, or even worse performance than your old card for lower end systems.
Also, I've read that you can get the mac version (for considerably cheaper) and flash the BIOS to make it think it is the PC version. I *have not* tried this, so it is at your own risk to do this. Check out
www.voodoosource.net for some info on it there, there are some really detailed posts about ppl doing this. I'd probably opt for the pci retail for an extra $20 bucks....just for the peace of mind. For people with PII's below 400, you might even consider getting a v3 3000 pci for like $30-40 bucks. From what I've read, those things were extremely well-made, and do really well over-clocked. I've seen some bench-marks showing it beat the v4 4500 pci in fps(of course it is 32-bit vs 16-bit), but still very impressive for an older generation card. I've got my current v3 2000 pci OC'd to 165 (from 147 default) with no extra cooling, and its been running fine for 2 years.
Hope this helped some,
Chiz