To go to the very basics, the number of cores is the no. of tasks a processor can do at a single time, and the clock speed is how fast it can do them.
Now, a 2.4Ghz quad core will be faster than a 2.8Ghz Dual core if the task can be split into 4 parallel tasks
Performance is a mix of processor generation, no. of cores, cache, clock speed and many other factors.
Hyperthreading is when a single core processor has some extra hardware which lets it behave as a dual core for certain tasks.
Multithreading is when a Program makes use of multiple threads to do its work
There arent CPU's in a core.. there are cores in a CPU
I'm assuming that the processor architecture is same..
A 3Ghz Pentium D vs a 3 Ghz i3 -- the i3 would win
(thanks to sidran)