Basically, everything you've listed is the same with the exception of
the mobo, cpu, and vid.

I'm voting AMD. But......

If you are concerned about PCI-E, why not get an Athlon64 mobo that
supports it? (Asus A8N-E, etc.)

Is cost an issue? If so, I'd drop down from the 4000+ to something
along the lines of a 3400. I don't think the performance difference
will be a major issue....and you can use the extra $$ to get the N7800.
Not to mention you can upgrade to a dual-core in 6 months without
paying the "new technology" tax...and sell the 3400 to people currently
running on the Athlon64 2800's and 3000's.

Of course, if cost isn't an issue, why not go SLI and grab two N7800's
??!?

As for the case, might as well upgrade to the Antec Sonata II (which
comes with a 450W power supply). The price of the new case is on par
with the "old" version, and supposedly they've worked out some of the
bugs.

I read a review recently, and it looks like top AGP cards are still
outperforming their PCI-E counterparts. Can't remember where I saw
this, though (anandtech or tom's hardware). I'm sure this will change
soon, but it's something to consider.