This topic was discussed here, but I discovered today that there actually is a way to edit the list of MSI files and .NET runtime options on the prerequisites page in Wise Installation Studio 7 (build 126.96.36.1999). I wanted to add .NET 2.0 SP2 Framework to the prerequisites, which you by the way can download here.
I copied the Framework setup to a folder that I created in: <Wise installation directory (usually C:\Program Files\Altiris)>\Wise\Windows Installer Editor\Stub\DOTNET2.2.30729
DOTNET2.2.30729 was the folder that I created.
The different versions shown on the prerequisites page is picked from an ini file in the Windows Installer Editor directory. It is named dotnet.ini.
I added the following section to dotnet.ini:
Now I can choose this runtime from the dropdown list on the Prerequisites page.
Note that any new added runtime cannot probably be handled correctly by Wise if it requires different command line options than the older ones. This seems to be the case with .NET Framework 2.0 SP2 also, because it is not installing silently.
As far as I know, this does also not mean that Wise in any way can benefit from the SP2 version of the framework by itself. The .NET functionality in Wise is still based on the older 2.0 version (WiseDotNet 2.0.2469.22324).
Disclaimer: This is not supported by Symantec/Wise and by following these instructions you take the responsibility for breaking your installation, your PC, your dog eating your cat etc. etc.