The only reason to not go for the latest version is that it can complicate deployment.
.NET 2.0 is installed automatically via Windows Update, so you can expect it to be on the target computer when your deploy your application. .NET 3.5 is not being pushed automatically yet, so you need to distribute the framework with your application. This will probably change in the near future.
If you are not concerned about deployment, then go for the latest version. The fact that you target the .NET 3.5 framework, does not mean that you have to use all the new technology. For instance you can still use Windows Forms instead of WPF, but that is another question.