Linux supports SMP pretty well. You'll have to make sure you have SMP enabled in your kernel of course
Multiple processors are not much help on large, monolithic, programs. They can be tremendous help on threaded apps.
Even if you don't go with a multiprocessor machine I'd start looking at making your large, computationally intense, programs as parallel as possible. It appears parallelism is the future.
BTW... I love my dual Opteron
I'd recommend one of those bad boys to anyone