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A few people have expressed a desire for an MSI-based Windows installer for PuTTY. Apparently MSI is easier/possible to deploy via various software deployment mechanisms (Group Policy, SMS, Active Directory), compared to our current Inno Setup installer.
WiX is a free thing that will create MSI-based installers. This page lists some others.
Update: we released an MSI installer for 0.67 shortly after it was released (so 0.67 is available in both Inno Setup and MSI forms); we plan to retire the Inno Setup installer in future.