Matlab 6.5 supports an unattended installation by running "setup.exe -if <inputfile>". The input file is a customized installer.ini file. A sample installer.ini file is provided on the Matlab CD. Details are available in the header of the installer.ini file.
I found that the unattended setup works as described by the vendor, but it didn't provide the flexibility I need. I repackaged the setup into an msi with Admin Studio 5.
I ended up using the Mathworks installer with this. To package all 32 toolboxes we use, it would take forever and be very complicated with WIse. I wrapped it with SMS Install Script to do other things I needed.
The one drawback was that I had to create a ton of .exe and .ini files. But it works great.