Well, I guess it depends on what you're going to do with the box. If you're for ultra low power you'd have to wait until these ARM CPU boards (or similar embedded CPU) finally get some storage option. Low power can be reached probably with Intel's Atom and VIA's C7 ones (or successors, though be warned, their CPUs are okay but the other chips vary in quality, esp. when it comes to driver problems). If you need some more computing power something like the AMD 4850e/5050e does a fine job, though they should be quite rare today. But look around their successors, the Athlon2, there should be some models with nice low power consumptions available. I got my box with onboard (AMD-ATI) GPU and 4850e and a Seagate 7200.12 and 2x1GB RAM to consume about 45W idle and 75W max.
Maybe the new cores can go down even more, I guess you can have unused cores switched off (CPU hotplugging) and seperately downclocked. Should you still need more computing power look a class higher to the Phenom 2 or some intel device.
I must say that I'm very pleased with my 4850e as an allround machine. Passively cooled btw.. But I guess the next generation Athlon is even better and, not unimportant, available in stores.
I'm not familiar with RAID and I don't have a good opionion about RAId (esp. mode 1 and 0) but if you'd like performance look for a hardware solution.
Asus ... phew. I'm not so sure about them. Gigabyte offers also fine boards afaik, and if you look for a pro board go for Tyan. But take some money with you.
Multicore is nice in any case since you're going to use Linux so it will make use of it. And the new CPUs can have their cores clocked individually which is a good thing. Still, if you just use it as a file storage server you won't really need multiple cores unless you have a really high throughput of data.
Stop TCPA, stupid software patents and corrupt politicians!