I recently discoverd that there is a bug in the dutch .Net assembly that effectively breaks NavigationWindows on dutch vista SP1 or higher. See for details this link
A hotfix is available, but how can I distribute this with my ClickOnce application? I am appalled that this situation, that seems to be known since february, has not been remedied. I am also puzzled: any dutch vista computer running SP1 or higher will crash on a wpf Navigation apllication, so there should be more outcry about it. Is no one writing Navigation Programs?
I don't think there is any way to deploy a hotfix as part of a ClickOnce application as it would violate the entire idea of click once. That is to be a zero impact installation environment.
What you could do though, is add a section to your program which checks for the particular flaw and then pops up a message box / form, requesting the user to deploy a particular hot fix. Including a link should make the process pretty straight forward. Not an ideal solution but it should help to alleviate your particular problem.
If you put together a new deployment package and set the "hotfix" file as one of its prerequisites, you may be able to get the result of having the user need to install the hotfix prior to the user installing the updated version of your app.
I tend to think, however, that a bug in the .NET framework should be outside the scope of your ClickOnce application's support requirements. If this is an intranet app, you should probably work with your IT department to get the hotfix deployed out to your users as a separate effort.
If your ClickOnce app is on the internet, however, then either JaredPar's suggestion (a check/dialog inside your app's startup to see if the hotfix has been installed or not) or just a notice on your website with links to the hotfix should be sufficient.
Good luck, I recently learnt web deployed ClickOnce suck.
We too are looking for a more efficient way to patch a ClickOnce app. Currently hitting almost 30MB in size :(
Currently I am looking at using bsdiff on a CDROM deployed app, patching the installation sources, perhaps only supporting minor updates (eg 1.0.1 - 1.0.2).
There are still many possible issues to think about.