Doesn't matter much tbh.

I myself use PCI if I have an available PCI slot, else I use ISA. PCI is a bit quicker with 100 mbit.

For me it depended on what I had in my other slots. Since I had all my PCI slots full I had to go with an ISA card for the NIC.

My preference would have been PCI to eek a bit more performance out of LAN transfers.

It would help if you mentioned what actual card you are considering using. Then we could point you to drivers.

Save the 3com card for an ISA only machine, 486 or older. Those cards will also work in an 8-bit slot, so if you have an XT class machine this will get it online. Check out mTCP for some useful TCP/IP apps that will run on an XT.

The PCI card will perform much better than the ISA card, if you have PCI slots available and can find drivers for it. There are probably packet drivers for DOS available for whatever it is.

My upcoming retro rigs approximately has 2 PCI and 3 ISA slot. Should I go to PCI?

Does the performance really matter, or will you only occasionally transfer data over ethernet?
If you are talking about a 100MBit/s card then not only the transfer rate will be limited but also the CPU will be quite busy if you transfer a lot of data. Even a faster CPU will approach 100% load if you try to saturate the ethernet, and you still will not reach maximum 100MBit performance.
With PCI cards it's possible to saturate 100MBit, but it depends on the chip how high the CPU utilization will be. For example if you switch from Realtek to Intel or 3Com you might cut CPU utilization in half. I did change my Ethernet card once for this reason. (Realtek is good for compatibility/drivers, though.)

About drivers: If you can't find native WfW 3.11 drivers you should still be able to use a DOS packet driver in combination with Trumpet Winsock. Of course native drivers are preferred.