To deploy the .Net Framework do the following:
.Net Framework 4.0
Package your dotnetversion.exe up as a custom software deployment (for example: dotNetFx40_Full_x86_x64.exe)
Under the 'Install command', use the following:
start /wait ??SOURCE?? /q /norestart
Note that the " " has been removed from SOURCE, the installation will fail without removing " " as it affects the following /q 3.5 SP1 (Windows 2008 R2)
.Net Framework 3.5 SP1 (Windows 2008 R2)
Since .Net is already packaged with Windows 2008 R2 it has to be installed as a "Role" instead of an executable, similar to IIS.
The Install command will be:
start /w dism /online /enable-feature /FeatureName:NetFx3
The above is case sensitive for the package name so make sure it's "NetFx3".
.Net Framework 3.5
A sample script to do a full install of .NET Framework 3.5. can be found here.
Here is an example of what the Depot Object will look like: