I have now the same harddrive used on all FC versions since FC2 and I always kept my personal files. The /home folder is set as separate partition, an like
acid_kewpie mentioned, format all the rest except this one and you will be fine.
Another thing I do is remove all hidden files and folders or other config files withing my /home/boby/ folder, I mean for example .gnome, .kde, .mozilla, etc.
You will loose all installed applications because they are installed usually in the system partitions, but documents, music, and all your private stuff won't be removed as long as they are in /home and it's a separate partition.
Note: A backup is always safe