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No, I say B! The RAM is faster, the CPU is faster.
For what you will be using it for, the 10K RPM Raptors will be fine. It does sound like your apps are CPU and RAM heavy, so definitely go with B.
CPU vs CPU, the Dual Core will kick the Dual Xeon 3.0's ass.
Quadcore vs Dual Xeon 3.0 will rape.
My favorite CPU right now is the Core2Quad Q6600... it absolutely monsters through everything and is actually one of my best sellers. It sells so well that I keep running out of stock damnit!
Definitely get Server B, with Core2Quad Q6600.
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