If your machine will do PCIe I'd use the PCIe NIC purely because of upgradability. Also, if I were you, I'd give it a gigabyte of RAM, especially with a dual core. You'll be able to do some neat stuff if you can give it some more RAM (some 3rd party packages use a lot of RAM, I've found)
That'll be perfect as it'll give you a port for both wan and lan. I have the quad version of this in my pfsense box and it works no problems. You can get them cheaper on ebay too.
Just remember that it's a pci-e 4x and so you'll need a free 4, 8 or 16 slot to put it in.
I have a 1x and a 16x, so I should be fine. However if I just used a single port NIC, would I use the Intel for the LAN? and whatever onboard for the WAN?
I'm going to try to go for a 2 x RJ-45 but money is tight for me. Jobs for minors blow... May have to wait until I get my tax returns to do this right.
Ideally you'd have Intel for both, but it doesn't really matter. The Intel nics have less CPU overhead but unless you have gigabit internet or a really slow CPU then you probably won't notice a difference in performance between the two.