Not a professional here... take my comments with grain of salt.
My understanding is that most applications run multiple threads. However, the threads may only worked on one at a time with CPU going round-robin through all open threads. This would be the case of an application not taking advantage of multiple cores.
In an application that takes advantage of multi cored CPUs, then more of the threads can be worked on simultaneously. So, in your example, a single core machine will work through each of the 39 threads one at a time. In an 8 core machine, in a perfect world, the machine would be able to work on 8 threads simultaneously. All 39 threads would be distributed (more or less) evenly across 8 cores. I forget if the Mac Pro CPUs support hyperthreading, which enables each core to operate on 2 threads - effectively making an 8 core machine into 16, and a 12 core machine into 24. Wow! Of course managing all of those threads takes it toll with overhead management.
A year or so ago Apple introduced a new technology called Grand Central Dispatch that promised to make it easier for developers to make their applications multi-core, multi-processor aware. I don't think we've seen much develop on that front, however.
My take is that sometime this year (I'm optimist) this Grand Central Dispatch will start being leveraged more and more, making my 2008 octo-core get relatively faster as more of it cores are utilized. So far there aren't a lot of applications that max out all 8 cores, but I have a couple. I think Lightroom may be one - for some operations. Hmm, I know I got really excited once seeing all 8 cores 100% once - but I can't remember what I was doing..... anyway.... What it means for me is that I can run several applications (that individually don't use 8 cores) but when run at the same time OS X will distribute the work evenly.
all of this is ymmv, and imho, and afaik, and iirc - - of course