I have a Motorola Droid (v1) and a docking station. When the phone is docked, it automatically runs the Clock app, which isn't very configurable. Are there any alternatives to the Clock app, or is there any way to configure the phone to run a different app while docked?
After you install an app that takes over the Dock intent it will ask which one you wish to use as default.
The one I use is called Gentle Alarm which has a nice Dock display and some additional alarm features. It is however a paid app. I know there are several free apps out there as well.