This is timely. I've been planning to do some system upgrades, but haven't been paying that much attention to the last couple generations of processors. Here's a nice overview of the situation and a buyers' guide.

I went through a similar situation about a year ago when I built my personal tower. I knew I wanted an Athlon 64 (because 64 bits just sounds so cool, and I'm sympathetic to an innovative "David" like AMD over Intel's "Goliath.") But the question is whether I should go with the standard Athlon 64, the 64 X2, or the FX. In the end it boiled down to my minimalist needs: the system would be used for very little gaming or video editing.

I also went with a slower clock speed but got a gig of RAM and a 300 gig hard drive. The soundest advice I've received in designing a system is to save money on a slower clock speed and spend what you've saved on RAM and hard drive.

If you like a complete system-level overview, i prefer something like this:
http://www.sharkyextreme.com/guides/MVGSBG/article.php/3649521

They put it together based on best price/performance ratio. Even though its gaming oriented it would work well for other apps as well.

I'm an avid reader of Tom's Hardware guide. From that, I'm convinced the AMD is still the best bang for the buck, but the Intel Core2Duo is the best processor in overall performance. I went with the E6400 and I'm complimenting it with 4GB of PC6400 memory (4 x 1GB). I'm building on the Asus P5B-VM mainboard to build a portable media entertainment system, that is extremely powerful for other stuff. The large memory is to support Virtual PCs for testing server farm configurations.

I decided against the 64 bit, because some peripherals are still having problems with the bus. I'm hoping those are resolved soon, as 64 bit really is the faster overall platform.