You can do a lot from a live CD. Get a live CD (Knoppix is very popular and works very well) and you can save the /home directory.
You can split the partition, and put /home onto one half of the partition. Then install FC3 on the other half and copy everything back.
Or, when installing FC3, mount /home on the partition with the files and DO NOT format it. You WILL lose the data if you do.
Or copy /home to an external hard disk if you have one. Restore it after reinstalling FC3.
Or copy /home to a different (can be Windows FAT32) partition and restore it later.
Or copy everything without a live CD if you have Windows. Install explore2fs
and copy everything to the windows partition (either FAT32 or NTFS) and copy it later.
I don't think you can save applications, though. But you can save settings, options and configuration files, like games' high scores list. To do that, just copy /home like I mentioned above, but make Kqnqueror (or whatever file browser) show all hidden files and folders. Copy them and restore them just as you would to to the data files.