What is the minimum I need to add to a .NET 2.0 WebSite's web.config to make it .NET 3.5?
Visual Studio adds all the config sections and script handlers, but if you aren't using those are they are really necessary?
Is there a command line tool to "upgrade" a .NET 2.0 web.config to 3.5?
There is a good description of the 3.5 web.config available here: http://www.4guysfromrolla.com/articles/121207-1.aspx
The assemblies and config sections are important because they tell the runtime to use the new 3.5 dlls instead of the 2.0 dlls
The codedom section tells the compiler to use 3.5
If your not using ASP.Net ajax you can probably skip the rest. I've never tested that though.
It depends on which features you want to include. Most of the 3.5 ASP.NET extensions are optional. You will want to include the assembly for System.Core and System.Xml.Linq. You will also to add compiler support for C# 3.0 if you plan to use that in your code behind. If you're deploying to IIS 7 there are HTTP handlers for the ASP.NET extensions and script modules.
I don't think either of these answers are definitive. The 4guysfromrolla reference is helpful.
Deploying .NET 3.5 to 100+ sites will be a pain. You can't just upgrade the server to the new framework, you have to upgrade the web.config of each site. As far as I can tell, there is no command line tool to do it.
If you want to upgrade every site on a server you could probably make changes to the machine.config