The Core2Quad is a newer processor - but it actually isn't really a "Server" processor - more suited for desktop applications (this will get quite a bit of argument going). The AMD Opteron is actually a Server processor, and so is the Intel Xeon. However, you have quoted the Opteron 246 which is quite an old processor and AMD have since release much better DualCore and QuadCore CPUs for Opteron series.
Verdict: For me you can't go past the 8gig of ram - so the answer in this particular case would be to go with the Core2Quad Q9300 with 8Gb Ram.
Side note: I normally would prefer Intel Xeon series or better for QuadCore.
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