I'm downloading the update right now and I would like to know if any of my files or app gets deleted after this update... I'm sure many people here already installed the update so what can you say?
From my upgrade experience, nothing has been lost in the process. All application settings are the same, all the applications are there and all the files are still here.
Upgrading an operating system should never touch your personal information and your installed applications unless you are doing a clean install, but if you are simply running the "Install OSX Mavericks" application, you have nothing to worry about.
However, the only thing that does get deleted is the installer itself once you have finished upgrading. If you would like to keep it to either create a bootable recovery USB or use the installer to upgrade other Macs you own, you can either copy it to a USB or some other form of storage besides your boot hard disk or simply make a copy of it in a compressed zip folder which wont be deleted regardless of its location.
Hope this helps!
I noticed that the Finder favorites were reset. I had some custom folders in the list of favorite before the update and now they are gone. I KNOW that I had a favorite for Dropbox and it was missing after the install (I chose to move my Dropbox folder to another drive so it isn't the favorite created by Dropbox). There was also a new favorite for "Deleted Users" that I didn't know existed before.
I tried going through time machine history to see when it changed, but it doesn't seem like the list of favorites are changed with time machine.