Those hidden files and/or directories won't contain the apps themselves, they'll contain the user settings/config/data for each of those apps. If you want to keep the apps and all their data, etc., you'll want to back up all the 'dotfiles' in your home directory plus any installation files (the .rpms, .tgzs, etc) for the apps in question.
What I tend to do when moving to a newer version of Fedora is leave everything in /home intact but do a clean install of the new Fedora, formatting / in the process (to do this I need /home to be a seperate partition or logical unit than /, a hint I picked up long ago). I then install my favourite apps from wherever I previously got them from (yum repos or manually install rpms or tarballs). This gives me a nice, clean installation but because I keep my dotfiles the desktop and apps will still be configured just the way I like them.
Asus Eee PC 901, 2GB RAM, 20GB SSD + 16GB SDHC w/ Fedora 11
HTC Hero w/ Android 1.5 (MoDaCo Custom ROM 2.2e)