After I run Analyze cleaner, I get a list of files to be removed. Such as: Application Office 2003 26KB 49 files and Multimedia Adobe Flash Player 309KB 1139 files.

When I then RUN CLEANER:

Does this mean that I will delete all my data file? Does this mean the applications will be removed? If so How can I select which ones will be deleted?

I think this should actually be included in your FAQ's.

The programs wont be removed. Only the temp files used by them. In CC you can goto the Applications tab to select or not, various applications installed on your system.