The Core2Duo will beat that Pentium 4 despite the higher clock speed of the Pentium 4. The Core2Duo most likely comes with more L2 cache, more L1 cache, has two cores obviously, and will also support 64-bit and extra extensions/instruction sets. 64-bit does in fact run a tiny bit faster than 32-bit as well.
If you have a Single Pentium 4 CPU, that second core is a hyper threaded core. It gives the impression of a second core and does provide a slight speed boost, but it's not two CPUs. If you really do have dual Pentium 4s though (which means that your box is probably server grade for it's time), the Pentium 4s should beat a single Core2Duo for most tasks.