<p>What is the minimum I need to add to a .NET 2.0 WebSite's web.config to make it .NET 3.5? </p>

<p>Visual Studio adds all the config sections and script handlers, but if you aren't using those are they are really necessary?</p>

<p>Is there a command line tool to "upgrade" a .NET 2.0 web.config to 3.5?</p>

There is a good description of the 3.5 web.config available here:
https://web.archive.org/web/20211020153237/https://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 you're not using ASP.Net Ajax you can probably skip the rest.  I've never tested that though.