This is really handy when changing ROMs.

If you need adb setup on your Debian GNU Linux system go here
Once adb is functional:

mkdir apks
cd apks
adb pull /system/app
adb pull /data/app
You can simply install them from your directory
cd apks
for i in *.apk; do adb install $i; done
Any apk's that are already installed on the device will simply fail to install again:
511 KB/s (430701 bytes in 0.821s)
pkg: /data/local/tmp/com.twistedapps.wallpaperwizardrii-2.apk
Alternatively, you can tar them up:
cd ..
tar czvf `date +%m-%d-%y`-apks.tgz apks/
Push them to the device
adb push *apks.tgz /sdcard/
And install from the device
adb shell
tar xzvf *apks.tgz
cd apks
for i in *.apk; do pm install $i; done

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