+1 for the quad-core. Not all applications will be able to make effective use of Hyper Threading.
Hyperthreading should be transparent to the OS and programs - anything that can take advantage of a quad can also take advantage of a hyperthreaded dual. That having been said, the quad is a better choice unless the dual has a significant clockspeed advantage. In other words, I'd take a 3.2 GHz core i3 over a 1.8 GHz Phenom, but if the clock speeds were even remotely close, I'd get the Phenom every time.
Oh, and hyper transfer is not hyper threading. AMD has hyper transport, but that's different too.