In store: Probably only stock Imacs so you would not be able to get the 256VRAM. Call and ask though, some might have one or two. If they have one, check in the store to make sure it actually is a 256 as some users have found that you may buy 256 but not get it. Defective items bought in stores I would imagine would have a faster turn around than online since you dont have to ship it. But even online apple does a fine job in assessing problems.
Online: Amazon has a $150 rebate and you do not have to pay sales tax. As with the store I do not think you can get a 256VRAM card though. If you are eligible for a student discount at apple.com it would be about the same price with the upgrades as amazon with the rebate. A little more expensive. When I emailed macmall the following system would cost $1824:
Imac Core Duo 20-inch
1GB RAM
256VRAM Card
250GB HDD
Normal Keyboard and Mouse not BT
Then add around $30 for shipping, no sales tax though.
And no I dont even own an iMac yet(ordering after vacation in late Feb.). I have just spent enough time on these boards to make it look like I do.