Soon to be Power Mac owner with a couple questions.

RAM and hard drives should be bought 3rd party.
Definitely go with ATI 4870.
HOWEVER, $300 for 12GB (6 x 2GB) is actually decent enough I would go with it this time, and it should be enough to hold you while 4GB price etc and quality improve and if you outgrow and need more. I think heavy CS4 users may need more possibly.

Most everyone is very happy with what they chose as far as processor performance, and Intel, Apple and developers are trying to tweak and learn how to best leverage multi-core and multi-threading (HT: what is old is new again) to best use. There are some tests that try to qualify raw cpu test performance, but again, real world is where it matters. See Barefeats which has done over a dozen tests on the 2009 Mac Pro.

I think someone could be very happy with spending just $500 and getting 4-core (8 threads with HT) 2.9GHz model and spend the saving on RAM and disk drives EXCEPT then you have to use 3 x 4GB (tri-channel) or take a slight hit with dual-channel when using 4 x 4GB. That is the only down aide, next to impossible to get beyond 16GB RAM.

Last year's 2008 3.2GHz isn't quite as fast, the same price ($3300) as =2.26 and has 8 DIMMs for 32GB RAM.
http://store.apple.com/us/browse/home/specialdeals/mac/mac_pro

If I was building a workstation I would have opted for 6 memory channels for the 4-core, 12-24GB, and 12 DIMMs for dual, 24-48GB RAM. We've had 32GB config for 3 yrs already.

SSDs are a nice big black hole to spend on and get real performance boosts.

Snow Leopard should help make better use of multiple threading, meaning, even a 4-core / 8-thread will (should, eventually!) see higher cpu usage (and hotter, as HT does ram up temps and watts).

A poorly written app like iTunes for some reason doesn't like HT and will push one cpu to 100%. Previous to 10.5.7 (10.5.6+ build) CS4 ran slower on dual cpu, so that was quickly fixed, can't have that! but the kind of things to expect. When the Mac Pro first came out, the first OS update improved numbers by a full 20% (10.4.8 from late '06).

Most people and benchmarks have a touch time translating $1400 and 400Mhz (x 8 = 3.2GHz though) into real results (finish a project in less time that matters). Again, spend the money on storage, RAID controller, drives and cases.

Mac Pro and Intel requires more RAM for the same task as PPC did.

http://browse.geekbench.ca/geekbench2/view/115605

Warning on Migration Assistant:
http://discussions.apple.com/thread.jspa?threadID=435350

The GTX 285 from Nvidia is not BTO, $449 but has more VRAM which can help and once its drivers improve (and that may depend on SL) it would be really nice to see it as BTO option alongside the 4870.

http://www.barefeats.com/nehal03.html

If you're working with raw 1080p video you'll have to go for quite a speedy RAID array, SSDs might not be entirely necessary, but two or three speedy discs in RAID0 would be nice. (go for RAID5 if you want to spend money on a hardware RAID controller and 4 discs.)

If you're working with pre-processed or compressed 1080p video your storage doesn't need to be as fast.

You'll probably want quite a bit of memory, though. I don't know if higher CPU speeds are noticeable with your kind of work. I rarely see any CPU core reach 100% and I have the basic model 8-core Mac Pro (2.26Ghz).

The 4870 BTO is a good deal at $200. However if you are running third party monitors (non-apple displays) I would read through some threads here to see if your particular display has or has not seen graphical issues.

This was a big problem in 10.5.7, has it been fixed in 5.8?

If you are running third party, perhaps the 285 would be a safer choice. As hatter said, the drivers should get better.

http://store.apple.com/us/product/TW387ZM/A