Stuffit Standard Edition 8 works all around for me. I bet your problems launching applications are because you don't have permission to launch them. I ran into this a while ago with some .sit archives. You need to go into the app package and give yourself (as admin) permission to execute the main binary, and read all the package contents. I don't know why that happens sometimes. If there was compression corruption, it would not just affect applications. A compression algorithm doesn't care what kind of file it's working on.
StuffIt Standard 2009
Compress or expand most archives.
Version: 13.0.2