Native applications on IPhone seem to be more usable and a web based experience seems to be totally different than IPhone experience. I am already aware of iUI framework but am wondering how the community is tackling with this problem.
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1We just wrote such an application, so it is possible. Even though written for both MobileSafari and desktop browsers at the same time, the interface design was essentially ported from mobile to desktop. On the desktop it was a narrow but taller interface, without touch events. The whole thing was basically one page with javascript used to hide and show content in such a way that it looked like you were switching pages.
In another case, porting from an existing desktop site to mobile, we chose a complete redesign. The desktop usage and flow was too different from what would work on mobile, so it became two separate interfaces to some shared resources.
It is possible, but deciding wether it is a good idea mostly depends on what you are presenting. Can you get away with a single column on the desktop that can be narrow enough to fit on mobile. Can you use a simple enough navigation model for mobile that will not frustrate desktop users? There is some fairly low threshold of complexity beyond which it is better to separate mobile and desktop. If all differences can be encapsulated in css, then a single application is probably fine.