I have written two articles on this. There is the upgrade guide and also the other post that explains why it occurs.

A quick summary of solutions:

1) If you have Cydia still visible you can install Quickgold and simply launch the hidden apps. You can launch bossprefs, poof, or such and unhide it.

2) You can install SBSettings and unhide any apps that are hidden.

3) You can launch settings app and disable / reenable restrictions which should unhide most of everything. (You will then need to use poof, bossprefs, or sbsettings and rehide what you want hidden).

4) If you cannot install anything because Cydia is hidden, you can use apt-get install quickgold from the SSH prompt

5) In the most drastic case where you also do not have SSH, you can use iphone browser and delete the file located at /var/mobile/Library/Preferences/com.apple.SpringBoard.plist. Then reboot.