Yep. What you have internally has no bearing, you can format the external drive either FAT32 or NTFS and it'll work fine. You can also use either USB 2.0 or Firewire. If you're using it a lot, I suggest Firewire, I find it has faster throughput by about 50% and much less processor overhead.
Copying large files using the USB interface, my machine really bogs down, however the same copy with Firewire isn't even noticeable. My machine is a P4-2.4, so it's not that slow...
