Hi Jon,
Windows Installer is a traditional installation technique. ClickOnce is a new installation technique that is introduced with .NET 2.0. Using ClickOnce, we can publish an application to a web site, Ftp site, shared UNC or CD. We can select installing the application on the client machine or running the application online. If you install the application on the client machine, the application will check if there's new version available in the publish location when it is launched next time. If yes, it prompts the user to upgrade to the new version.
> I would also like to be able to have the installer install the dotnet 3.5 redist and the SQL Server Express 2005(8) files needed to run the application.
Whether you use Windows Installer or ClickOnce, you can include the .NET Framework 3.5 and SQL Server 2005 Express as prerequisites.
For your scenario, I advice you to use ClickOnce to deploy your application. For more information on ClickOnce deployment, refer to the following document:
"ClickOnce Deployment Overview"
http://msdn.microsoft.com/en-us/library/142dbbz4.aspx
Hope this helps.
If you have any question, please feel free to let me know.
Sincerely,
Linda Liu