WinMerge 2.x use a InnoSetup installer and we played with a MSI installer. For WinMerge 3.x we should use from the start the MSI packages.
Mac OS X
For Linux there are several packaging formats (RPM and DEB being the most popular). In principle same RPM or DEB package should work for all RPM or DEB based distributions. In practice every distribution wants their own packaging (dependencies, package names etc wary).
Until somebody is interested in packaging WinMerge for distribution our preferred installation method will be by building it from sources. We need to add installation support for our project files.