Obviously it depends on what you are using your machine for as to which mini might be best. Perhaps I missed it but I don't see people blindly choosing one option over another but rather sharing thier experience or recommendation based on someone's question which describes the "what" to some degree.
As to the faster processor having an advantage if you are using single threaded software, that's only true if you are also single tasking. Same for the turbo advantage, which only exists if you are using a single core. If you are running multiple single threaded applications, the OS will spread the load across threads/cores and depending on how many simultaneous threads you have running the slower processor with more cores can still have an advantage.
As to virtualization, I'm not aware of any Mac/OSX/VM software/hardware combination that supports virtual IO. Yet VMware fusion and parallels both run great on the platform so not really sure how critical this feature is. When running multiple VMs extra cores sure come in handy for performance though as each VM can have its own core.
I'm curious about what you call the 29/59 issue. You mention it and go so far as calling the CPUs defective as a result but don't describe what it is or how it might manifest itself. Please enlighten us.
