i suppose the one problem that's always around has been the bundling of 'other stuff' with freeware. one can't blame the authors, after all they have to make a living unless they're truly philanthropic, but they should preferably make it clear that something more is going to be installed other than the software you want.
i think many of the pieces of freeware i've used / use did have an option for custom install where you could opt out. problem is that few people bother with custom install....