The supported apps will appear in your Applications folder. The unsupported ones will be put in a folder like /Unsupported Applications. Also, if you have GPL apps (i.e. not installed inside /Applications) like MacPorts, you'll have to reinstall/recompile.
After you upgrade it should leave all your apps & files exactly as they were previously. When I upgraded to Mavericks I noticed no changes to my existing apps & files - they were all still where I left them