Of the two choices you offer, 2 8800GT's would offer the best performance.
The 9800GTX is nothing more than a reboxed 8800GTS 512 with slightly higher clocks.
If you are still in the research process of your new build, keep in mind ATI and nVidia will be releasing their new products in less than a month. nVidia's new GTX 280 is supposed to be faster than a 9800 GX2 for only a little more than you would need to spend on SLIed 8800 GT's (taking into account $ saved off a SLI motherboard).
Recommend you wait the extra month before sinking your $$. If you don't like what you see then, prices for the 8800GT are expected to drop.
There are cheap dual slot 8800GT also. And really the single slots don't get that hot if you can put up with the noise.
As has been said, two 8800GT have a lot more performance potential. With current low prices, SLI 8800GT is the better option if you have an SLI mobo. They are even above an 8800U by a long shot. 9600GT SLI can beat a 9800GTX in most games, sometimes by a good margin.