I'm using CruiseControl.NET - this could be adapted for use in a Nant-only solution if desired. I call wfwi.exe which is included in the Wise installation and is meant for command line access (here's the Wise installer manual which contains instructions for wfwi.exe). Here's a snippet from my ccnet.config:
<!-- build installers -->
<exec>
<executable>C:\Path\To\WiseWrapper.bat</executable>
<buildArgs>"C:\Path\To\wfwi.exe" "C:\Path\To\Output.wsi" /c /p /s</buildArgs>
</exec>
<!-- build installer exes -->
<exec>
<executable>C:\Path\To\Wise32.exe</executable>
<buildArgs>/c /s C:\Path\To\Your.wse</buildArgs>
</exec>
And the WiseWrapper.bat allows the installer ProductVersion to be updated using the CC.NET build label. The entire contents of WiseWrapper.bat is:
%1 %2 %3 %4 ProductVersion=%CCNetLabel% %5