copy the information you want to save to something other than the partition on your hard drive you are reformatting/reinstalling on. If you only have one partition you could possibly make a new partition and move this data you want to save to it, then reformat the original partition and then you will be done. Another option is to save the data to cd/dvd/flashdrive/external hard drive.
A word of caution, don't bother trying to save games and applications as often times you will need to reinstall them again anyway, and generally you can either just redownload them or reinstall them from where ever you got them (cdroms and such). Only save stuff you can't easily replace. You might want to consider saving the "save game files" from your games of course. For that just do a google search to find how/where your game saves that information and copy those files (these files will generally be very small). Once you have removed this stuff from your data you want to save, you might find what is left willl fit on your flash drive.