You can change your apt sources to the FC5 tree, which I forgot exactly what the path is, but it is the same on all Fedora mirrors. You just change that path in apt-source, and do:
Then you have to fix all the problems, which shouldn't be too bad.
Read the man page for apt-source and apt-get before you do it, but that will upgrade, leaving your /home directory intact. The thing is you might not be able to go from FC3 directly to FC5, you might have to do FC4 in between. FC5 is a machine hog, too. Unless you have a lot of machine, don't even bother with it. I have it on a Pentium 4 3.0 GHz machine with 512 MB of ram, but FC5 seems to want more ram. Before I had Debian Sarge and it worked a lot better. But, this is my putz machine. I install all different distros on it just to check them out. I use a separate /home partition so I can do a full install and just not format /home.