Passmark benchmarks put the E5462 (2008 Mac Pro) at about 30% more performance then the 3210M (2012 Mini).
The i5 can ramp up to 3.1Ghz, but that's only when it's doing 1 thread, but when using both cores it will only go up to maybe 2.7-2.8Ghz. So it is more efficient of a core, but the E5462 has 2 more physical cores. So it can make up through brute force.
Which brings me on to Hyper-Threading. Hyper-Threading will allow the i5 to handle 2 threads per core, which will make it appear as a quad core to the operating system. But you have to understand what Hyper-Threading is doing. It allows the core to inject a 2nd thread into the core to use "wasted" clock cycles. So for instance if Thread 1 goes in and only requires 60% of the CPU to do its thing, another thread can be injected to use the unused 40%. So for light CPU usage, it's a fantastic technology.
But with HT when you load up the core with a thread, it will still accept a 2nd thread but there will be very little idle cpu cycles to go towards the 2nd thread. So the single core becomes a more traditional single core performance wise. That's where a true quad core will beat a Hyper-Threaded Dual Core.
