After a wipe your applications will still be installed, but configuration settings will be lost. You will also lose all user data (messages, contacts, calendar, etc). I recommend that your use Desktop Manager to make a backup of your device before the wipe.
A "normal" backup (via Desktop Manager) only backs up customer data, it does not back up applications that were loaded over the air. There is an excellent thread on the boards on how to back up EVERYTHING, including applications installed OTA.