Performance != Cores x Clockspeed.
Even on multithreaded applications.
There're many factors towards performance of a microprocessor.
A Pentium D 3.2 Ghz (dual core) would lose quite significantly to a Core 2 Duo 2.4ghz. This is because of its architecture. Despite the two processors having the same amount of cores, the same amount of cache, the Core architecture is faster. To describe in detail why it's faster would take me more typing than I really care to right now, I'll just give you a brief look at what factors you should consider:
Architecture. Check this first. Look for reviews of similar processors, just google its model number and it'll spit benchmarks out at you.
Clockspeed. Of course this is important, but only when comparing processors of the same architecture. I'm gonna go a little on the rough here and give you a brief idea of how several popular microprocessor architectures perform. 1 being the lowest and everything higher being better: (kind of 'rough n' ready' but whatever)
Netburst (Pentium 4/D) 1
P6 (Pentium Pro through Pentium III) 1.3
K8 (Athlon 64/X2) 1.6
Core 2 (Core 2 Duo/Quad) 2
K10 (Phenom)2
If all things were equal that's about how I'd expect them to perform.
L2 cache: The jump from 1MB to 2MB is far greater than 2MB to 4MB. This, despite popular opinion does affect performance in games, sometimes by a 10FPS difference depending on the scenario.
Number of cores: Only really matters when the software is written to take advantage of it - remember the kettles? Although, the extra cores can be used by background tasks giving whatever needs it a little performance boost. The extra L2 cache given by the extra cores can give some extra performance, too.
Hope this helps explain why x CPU can beat y CPU despite z scenario.