First and foremost, Service Packs for the .NET Frameworks. Every one of them has had at least one so far. The service packs cannot be applied to the application once "baked" by one of these utilities. Second, depending on how much of the framework your app is using, they can generate massive .EXE's for deployment. And, if you have a bunch of these apps built with the .NET Framework baked into each, the collection can suddenly have the same framework multiple times for each .EXE. I've heard of problems or total non-functionality of Reflection with some them, though I haven't bothered to test these claims either way.
A guide to posting questions on CodeProject[^]
Dave Kreskowiak Microsoft MVP Visual Developer - Visual Basic
2006, 2007, 2008