I have an application that I would ideally like to run on all iOS versions, however I think Apple accepts apps only from a version and above (3.0 I think, but not sure). So
Sometime last year, an Apple DTS employee posted (and later clarified) on the iOS Developer Forums that the App store would no longer be accepting apps with a Deployment Target lower than 3.0. That might indicate that a lower Deployment Target has or will become grounds for an app to be rejected.
I would never set the Deployment Target lower than that of the lowest OS version among the devices I plan to use to test the app before submitting it to the App Store.
Also, the installed based of devices which haven't been upgraded to 3.0 or above might be too microscopic to be worth a developer's time or effort (unless you happen to still have and use one for some reason).
ADDED in 2013: App store submission now requires that the app support the 4" display, which requires iOS 6.0 or later, which allows a minimum deployment target no lower than iOS 4.3