Personally, I would go with the AMD dual core for a couple of reasons.

First, as Grandfather has said, the dual core should benefit you when multiple apps or multi-threaded apps are running.

Secondly, I read a very in-depth article about 5 years ago, explaining why the Pentium IV was not as well-designed as it could have been.  I've tried looking for the original article without success, but the author made a number of apparently well-researched and technically plausible-sounding points about how Intel had taken shortcuts, such as cutting back on the size of the cache (the L2 cache, if memory serves correctly), and other design weaknesses, in order to get the chip to market in time.  I do remember that article giving me strong negative feelings towards the Pentium IV ever since.

You are correct that clock speed is not the final arbiter of performance, and in fact the article which gave the Pentium IV low marks made the argument that, although it had a higher clock speed, it was wasting a lot of cycles of processing time due to its design flaws, and therefore seemed faster only if you were comparing clock speed and nothing else.  Consequently, when the motherboard/CPU on our desktop computer had to be replaced, we went with an AMD chip.  Although the clock speed was somewhat less, the performance was excellent, and I've always been a fan of AMD since.