Ward sums it up nicely. Clickonce is very useful in some cases. One of the major DoD issues with it is that it requires to many permissions to run, does actually have to be installed on the users computer, and can only be installed to the users local profile. Which means that any thing that is saved to 1 computer is not available from another terminal, and if you re-image the system, all that locally saved material is gone.
Silverlight and .NET is THE choice now for enterprise solutions on a DoD level. Commanders like it cause its pretty and User friendly. IT likes it cause its non intrusive on the thousands of PC's they have to maintain. Any IT department is going to be much more responsive to. "Add a link to the home page" v. Install on 3k pc's.