So I made an NSIS Windows installer package for Data Comparisons. It's smart enough to check for the prerequisites (.NET Framework and Windows Installer) and only download and install them if necessary. Thanks to this technique and the fact that NSIS only has 34KB of overhead, the installer is just 310 KB.
I've used NSIS for past projects and I love it. It's extremely lightweight, fast, and stable. And since it's completely scriptable, it'll only do what I tell it to do.