This is exactly my dilemma.
The upside of the 6-core is its faster clock speed. Its downside is only 4 RAM slots … so to get 12GB of RAM, you’ll need to put in three 4GB RAM sticks (slightly more expensive than buying six 2GB sticks, but buy from OWC or Crucial – Apple’s RAM and hard drive prices are ridiculous).
The upside of the 8-core is the 2 extra cores and it has 8 RAM slots. Its downside is the slower clock speed.
My understanding is that FCP is currently a 32-bit application and able to use only 1 or 2 cores and limited in the amount of RAM it can address. But it’s due for a rewrite to 64-bit, and that should enable it to use more cores and RAM. After Effects CS5 is already 64-bit.
So given current software, the 6-core may have an edge. But given the 64-bit future, it’s a closer call processor-wise. And the 8 RAM slots on the 8-core may tip the balance in its favor. And you can use the $200 you’ll save by upgrading the video card (which Motion will probably benefit from). But it’s still a tough choice.