Although it might seem as though you can only use Microsoft's ClickOnce installers with IIS, this is simply not true, as all you need to do is set some mime types on the server.
The simplest way to do this is to add the following lines to a .htaccess file in the folder containing the ClickOnce files:
AddType application/x-ms-application application AddType application/x-ms-manifest manifest AddType application/octet-stream deploy
Once you've done this, your ClickOnce applications should install correctly. Since the release of Microsoft .NET Framework 3.5 SP1, ClickOnce applications work in both Internet Explorer and Mozilla Firefox. Earlier versions of the Framework will only run ClickOnce applications from Internet Explorer.
You may also want to add the correct mime types for XPS files, XAML files, XAML Browser Applications (XBAPs), and Silverlight 2.0 Applications. To add these, simply add the following lines:
AddType application/vnd.ms-xpsdocument xps AddType application/xaml+xml xaml AddType application/x-ms-xbap xbap AddType application/x-silverlight-app xap