UPDATE: I added migration steps for FileZilla client.
I installed my OS from scratch to a new disk after my old one crashed. Now I’m doing the reinstallation of various applications and migration of my user’s settings for them. I’ve collected a list of some applications and the procedure on how to migrate user settings (NOTE: I’m using Vista, so the paths to user profile are somewhat different from those on Windows XP).
Mozilla Firefox
Copy the contents of \Users\username\AppData\Roaming\Mozilla\Firefox\ from the old location to the new one. This will copy all of your Firefox profiles, including plugins, preferences, even the last opened URLs.
Mozilla Thunderbird
Same here. Copy \Users\username\AppData\Roaming\Thunderbird from the old location to the new one and open the Thunderbird. You’ll get all of your e-mails, email accounts, filters etc. Congratulations on good products, Mozilla guys
Yahoo Messenger
Copy the contents of \Program Files\Yahoo!\Messenger\Profiles from the old location to the new one. This will copy some your user’s settings and data (message history, for example), but I didn’t manage to migrate my Yahoo Messenger preferences.
Windows Live Messenger
The situation is similar to the Yahoo Messenger. By copying the contents of \Users\username\AppData\Roaming\Microsoft\MSN Messenger you can only migrate some of your settings, not all of them.
Skype
You should copy the subfolder of the \Users\username\AppData\Roaming\Skype folder which bares the name of your profile.
FeedDemon
Copy the contents of the \Users\username\AppData\Local\FeedDemon\v1 directory. FeedDemon will still ask you to enter your account information the first time you start it, but after going through this wizard, all of your subscriptions, watches and view settings should be migrated.
µTorrent
Copy the contents of the \Users\username\AppData\Roaming\uTorrent folder. This will include all of your settings and you will also be able to resume downloading of files from the last uTorrent session.
FileZilla Client
Copy the contents of the \Users\username\AppData\Roaming\FileZilla folder to migrate your FileZilla settings (like the FTP site list).