It depends on the core... Some cores (the more expensive ones) can do a lot more calculations per clock cycle - thus putting out more performance per MHz...
Think of it like the old AMD Athlons vs. Pentium 4's, an Athlon XP running at 2.2 Ghz could put out the same amount of work as a P4 running at 3 GHz (I don't remember the numbers exactly, this is just an example)... it's the same thing with GPUs.
As Jamin43 stated, it would help to know which GPUs you are looking at.