I'd suggest the following configuration:
Octo-core 2.8 GHz Xeon processor (the standard configuration)
Upgrading the processor costs a ton and barely helps. Downgrading to quad-core will save you $500 but you're losing potentially half of your processing power. If you're going to be stressing this machine, you owe it to yourself to go for eight cores.
2x1 GB of memory
Apple charges absolutely bonkers-insane prices for memory. Stick with the base amount and upgrade it yourself. It's not hard. Get matched pairs of DDR2-800 FB-DIMMs from NewEgg, ZipZoomFly, or OWC. A 2x1 GB set will cost you $50-$100, while a 2x2 GB set will be about $125-$175. I'd go for at least 4 GB on top of the included 2 GB.
Stock hard drive configuration
Again, Apple overcharges to a huge extent for hard drives. Just stick with the single 320 GB drive they ship the computer with and upgrade the capacity yourself when you need to. Western Digital has some of the fastest drives available - one or two 1 TB Caviar Black drives would be nice, or if you really need speed, a WD VelociRaptor is one of the fastest desktop hard drives on the market (but it tops out at 300 GB capacity and requires some sort of adapter kit to fit in a Mac Pro). I believe 1.5-2 TB drives are going to be available pretty soon too. Again, it's pretty easy to install hard drives yourself in a Mac Pro so there's no reason to buy from Apple.
NVIDIA GeForce 8800GT graphics
Shake makes use of your graphics card, and you'll want something better than the old Radeon HD2600 XT that ships with the Mac Pro. Not that the 8800GT is exactly a new card (it's more of a midrange card these days), but it's still tons better than the 2600. And unlike the RAM and hard drives, you can't just pick up a generic video card, so you should get this upgrade from Apple. Luckily it's not overpriced.
One DVD burner
Like the hard drives, you can upgrade your DVD burner after the fact. No need to pay Apple $100 for the privilege when you can just get a second burner from NewEgg for $25 (if you even need one).
I can't really speak to your other requirements but this should get you started.
EDIT: Also, like others have said, the Mac Pro is due for an update sometime this spring. I'd hold off buying unless you NEED it now. A new Mac Pro would likely incorporate Core i7 processors (significantly better than the current Core 2 Quad-based Xeons), better graphics, and a better standard HD/RAM configuration. The only downside (other than having to wait) would be that it would use DDR3 RAM, which costs more than DDR2.
