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Based on power consumption, system performance, support and quality of manufacturing. Results are based on my personal opinion derived from lab testing database response times for clients.
Two (2) Dual Core Processors
#1 Sun Fire X4100
AMD Dual-Core Opteron 2.6Ghz
Cost, performance, lowest power consumption in the industry and (my favorite) lower fan noise
#2 IBM eServer 326m
AMD Dual Core Opteron 2.60GHz
HP ProLiant DL360 G4p
Intel Xeon ( FOUR INTERNAL DRIVES)
Dell PowerEdge 1850 (good price)
Dual Core Intel Xeon 2.8GHz
HP ProLiant DL140/DL145 (good price)
Intel Xeon or AMD Opteron
Unfortunately, your best option for dual processors at a reasonably low power is hard to find in 1U form, at least pre-built.
The "consumer"-oriented AMD Athlon X2 chips (Socket 939 and now AM2) are a better proposition power-wise than the Opterons. The Opterons, on the other hand, are better-suited for servers. It's actually difficult to find a single-chip (which is all you need for dual CPU nowadays) Opteron server, though. There are some special lower-power Opterons, but them come at quite a premium, and also take a performance hit.
Even if you want to build your own, server-oriented Socket 939 boards (i.e. with built-in video, optionally built-in SCSI) are few and far between.
If you REALLY want low power, there are a small handfull of boards available that take either Intel or AMD chips that are meant for mobile applications.
If you don't need a speed demon, there are some additional options using alternative chips. (Non-AMD, Non-Intel.) But not dual. Surprisingly, these ARE fairly readily-available in pre-packaged form. Do a search for "short-depth server". There seems to be a niche for these short-depth (typically 14") 1U low-power servers. They can be packed into both the front AND back of a typical enclosed cabinet due to the short depth.