Titanium Backup will back up your apps (even protected apps), app data and system data. I do not recommend restoring system data when flashing but program and program data restores work fine (I do it all the time). Consider the pay version of Titanium as it has batch operations and many other great features.

 

100% on Titanium Backup...Get that...

As far as when you flash a new launcher, it is because the new launcher has it's own settings (I assume you mean all of your widgets/shortcuts are gone). This being the case, you will have to move everything back to it's proper spot after a new install...

 

Just a note on flashing (or just install) a new launcher - for best operation make sure you go into your old launchers and stip them of all widgets and icons. Widgets don't behave well when installed in multiple launchers (use the free program "Home Switcher" to access your other launchers).

 

Yeah especially when you use a different version of the same launcher..

I learned that lesson the hard way lol... i never knew i could fit so many widgets on the same screen. every one was doubled, and my main home screen had alot

 

why couldnt you just nandroid backup and then restore just the Data? I've done that a few times without issue