How do I make Unity remember which applications are in the launcher?

I've found the answer: dconf-tools and libdconf0 were not installed, so unity couldn't remember settings.

Use Software Center or apt-get to install:

• dconf-tools
• libdconf0

You may have a bug. I simply right click on the items in the launcher to pin or unpin them.

For those who're looking for a solution to make Unity remember settings after a GNOME3 update and reverting back to Unity, I have a solution which uses the above Q&A as a start.

If you've installed dconf-tools and libdconf0, you can run into a problem which is:

• when you try editing Unity's Launcher settings with sudo dconf-editor, you can find the right values under desktop > unity > launcher, but it seems to be read-only;

• when you try to use use gsettings, it says

GLib-GIO-Message: Using the 'memory' GSettings backend. Your settings will not be saved or shared with other applications.

then don't give up, you're only one step away from solving the problem!

This solution is quite fun; you will have to re-add the gnome3 team repo and install a package from there:

sudo add-apt-repository ppa:gnome3-team/gnome3
sudo apt-get update
sudo apt-get install dconf-gsettings-backend

[I don't really know why this works, but it seems installing GNOME3 stuff messes up the GSettings backends so much that it can't be repaired by only installing dconf-tools and libdconf0.]

You can check whether the settings are writeable by running

gsettings writable com.canonical.Unity.Launcher favorites

If everything is fine then it returns true and after a logout/login Unity will remember the settings.