limera1n and greenpois0n are out, and so here is some nice tips to restoring...
When you update your idevice from iOS 4.0.x to 4.1 it will wipe all your cydia apps, some people dont know about pkgbackup and other programs so let me show you a free alternative, and if you ask nicely maybe Secretss (developer of cyfix and switchrd) will make an app for it.
Cydia is a frontend to apt which is a package control. You do not need cydia, you can find and install everything easily without cydia, cydia just makes it easier and graphical 🙂
Before restoring make sure you backup your cydia repos in /etc/apt/ I usually just backup the whole folder and copy it to another machine.
Backing up your currently installed cydia apps.
dpkg --get-selections > cydiapackages.txt
This makes a text file with all your cydia apps installed. Copy this file off your iphone to a safe location.
Now you either updated or restored and you have jailbroken your device, installed openssh and you want to know how to restore all the cydia apps. Easy lets make sure we input the repos first either through cydia or through the command line and then do apt-get update. All repos you inputed will be refreshed
So now you have cydiapackages.txt and you are thinking what can I do with this copy it back to the iphone:
dpkg --set--selections < cydiapackages.txt
apt-get -u dselect-upgrade
Your iphone will now install EVERY cydia app you had installed.
Easier method just purchase pkgbackup off cydia and use it, it sends a archive of all the apps including repos to an email address.