Disclaimer: As usual, I am not responsible for any damage done to you or your device by these scripts. They're simply what I use to do my own stuff.
What it does
Copies the application installers to the SD card into a folder, and makes a list of installed applications that can be used to generate an auto-installer for them.
A rooted phone with Busybox (any JesusFreke modified update) and the Android SDK Tools (specifically adb).
Copy the included file onto the SD card.
Download it here
Make sure you're unmounted and unplugged
so that you can access the SD card.
Open up the Terminal emulator
Backing up Applications
Once you've run the script, you'll have two things on your SD card: the applications folder (/sdcard/app-apks) and the application list (/sdcard/applist.txt)
To generate a restore script
(Windows batch or Linux shell script) go here
As long as adb is running and connects fine with your phone (check with adb devices), you can give that page your SDK folder location and where you stored your application backup (on your computer) and it will generate an auto-installer for your applications. Save it, run it, and it will reinstall all your applications.
Easy. I'll make a new restore script generator a little later, I just whipped this up to have it done.
If you're going to back up your applications more than once, make sure you move the first backup off of the phone first, otherwise it nests the folders. I don't want to delete a directory off the phone if it's used already.