Most of the dual Athlon MP motherboards require registered ram which has a slight performance hit vs normal ram - so a dual Athlon MP 2600+ system won't equal the performance of 2 standard Axp 2600+ systems using normal ram. Someone that ran a dually during Phase I and compared the daily output of the dually to a standalone Axp cpu system could give their experiences - but you might be looking at a dual MP system being about 1.8 to 1.9 times the performance of a standalone Axp system.
The HT on the Intel processors doesn't double the performance of the cpu for DF; and if I remember correctly (please correct me) those that run two DF clients on a Hyperthreading system noticed - at best - about a 10% improvement over just running a single client (and may have done a little worse). HT is best used with 2 applications that use different areas of the cpu, rather than 2 copies of the same thing that will fight over the same cpu resources.
I'd opt for the dual AMD system - or two single AMD cpu systems and help the underdog provide us with a better alternative to Intel's cpus. I'm biased.. and freely admit that. And I have fewer problems with my AMD systems running win98se than I do with the P4s running WinXP.