That’s what I did— I bought a 2.4GHz 8-core from Apple, then had OWC upgrade it to a 12-core 3.33Ghz monster! Read my report. (I would have gone with a 2.8Gz 4-core for an upgrade, but at the time the upgrade paths were not clear).
But it doesn’t have to be a 2010 Mac Pro—have a slower 2009 model? No problem! While you can’t go beyond 8 cores in the 2009 models, you can go from 4 cores to 8 cores and/or a faster CPU. See the Mac Pro CPU upgrade page.
Here’s one use case where more fast cores kick some butt.