Not everything puts stuff in the registry beyond the scope of the stuff that gets put there for Add/Remove Programs and so on. So those things will still work (but won't appear in Add/Remove programs, or your Start menu).
Stuff that is dependent on, say, DLLs its installed into your OS partition, registry settings for specific paths and so on, are going to fail and will need to be reinstalled if you flatten your OS partition at any point.
Stuff that is dependent on, say, DLLs its installed into your OS partition, registry settings for specific paths and so on, are going to fail and will need to be reinstalled if you flatten your OS partition at any point.