All settings are stored in your home directory. All of the settings in particular are in hidden folders (CTRL + H to view hidden folders). This is where your settings are for all of your applications.
I synchronize my entire home directory to another drive of equal size in my computer. Two months ago my main drive crashed. I reinstalled Ubuntu and copied my backup data (hidden folders and all) from my backup drive to my main drive in my home directory. When I rebooted, I had my desktop background back, all of my personal pidgin settings, thunderbird, firefox, etc. Everything is stored in there.
If you want to simply back up personal data and NOTHING else, then just select your personal data folders - I'm throwing out a common example: Music, Videos, Pictures, Documents. That way when you bring your data back over, all you're bringing is Music, Videos, Pictures, and Documents. You wouldn't be bringing any hidden folders which contain your personal settings for your applications.
I strongly advise in the future when setting up Ubuntu that you split your root ( / ) and home directories onto separate partitions. I partition my drive out so I have 20gb for root ( / ) and the remainder (upwards of 400gb) to my home directory. Why is this beneficial? Ubuntu releases a new version every 6 months. Some people may think it's a pain to reinstall every 6 months, but it's actually not at all if you take the proper steps (i.e. partitioning your hard drive to root + home). If you upgrade to a newer version of Ubuntu, just make sure you mount the proper directories (root and home) to the proper partitions and DO NOT check "format" under your home directory's partition. That way when Ubuntu finishes installing and you boot up for the first time, your music, pictures, etc is already there.
Keep in mind, your home directory houses your personal SETTINGS, but the root partition is what houses the actual applications. So if you do this, you will still need to install your applications, however your personal settings (some of which may be for those same applications) are there and will be matched up after the program's existence is present. Make sense?