We just purchased an Athlon 64 with the dual core, and it makes a noticeable difference in encoding time, even over a regular Athlon 64... and MUCH faster than a fast P4.

The other thing I'd highly recommend is getting a Buffalo Terastation. It's a new, inexpensive Raid-5 storage server. We got the smaller one, about 500 gigs ($700, i think), but with Raid-5, if any one drive fails, you can still read all of your data, and install a new drive and it will rebuild automatically in the background... so for data reliability, it should be much better than even a primary plus backup drive.

We may be unusual, but we've had a *lot* of drive failures using external USB drive enclosures. My guess is the drives simply get too hot when they're on for any length of time. Most of those cases don't have any real ventilation or heat sinking, and so that may be causing them to fail prematurely. We still use 'em for backups and archiving, but we are switching to the Terastation for all of the online storage.

Other than that... I'd say a gig of ram, one or two 250G drives in the internal bays of your machine, fast processor, and make sure that your entire network is gig ethernet so you can move files quickly from one machine to another or from the terastation to the computer.