@Supermule:
If you want high throughput, do NOT use flash cards…. Use HD install.
CPU, I think, will suffer the most DoS attack.
SATA is the preferred disk, if you do not have SCSI available or SCSI is not an option at all.
Routing, NAT, firewalling, and shaping don't touch the disk at all. In fact, you could boot pfSense from the LiveCD and not see a difference past boot time.
DoS attacks come in many flavors. Some of them will be CPU intensive (single host causing an expensive calculation repeatedlt) and some will be memory intensive (lots of hosts all doing a single request will cause the state tables to grow wildly). If in doubt, buy the best CPU/RAM config you can afford and hope for the best. FWIW, I do high-bandwidth, few connection traffic with a 1GHz Celeron M and 1GB of RAM just fine.