I'd say get the E6400.
The Core 2 line is totally new and is going to have quite a lengthy lifespan ahead of it (well, in IT terms anyway)
The AMD line is wheezing along now compared to the Core 2, much like the old Pentium 4/D line has been wheezing along previously. AMD will be desperate to bring out new technology to help them compete on performance again, this means their existing processor line is likely to have a relatively short future.
I suspect Intel is holding back on releasing higher clock speeds until it needs to, waiting for AMD to make a play and then respond to it quickly.
Anyway, Core 2 is new technology and it's going to be around for a while, meaning you'll be future-proofing your PC much better. Get the right motherboard and you'll be able to upgrade to quad core later on (or maybe even beyond that, 8 cores?)