Please note: if you are using Ubuntu 10.10 backwards, with Emerald supplying the window border themes for Compiz-Fusion (or have Emerald successfully running in 11.04 onwards), read this guide instead.
If you occasionally find your title-bars or window borders missing from your programs and folder windows, it’s actually quite easy to fix, and there’s no need to reboot.
You will need to edit a Compiz-Fusion setting, so open System > Preferences > CompizConfig Settings Manager; if it isn’t installed, just run sudo apt-get install compizconfig-settings-manager in a terminal.
Once open, scroll down to the Effects section, where you will see Window Decoration is not enabled. Simply click the check box to the left of it, and you should see your window borders reappear.
Keep this in mind for the future, as certain things can upset Compiz-Fusion and you’ll likely be without title-bars again (especially if you’re playing around with settings, as enabling one Compiz plugin can disable another).