With compiz enabled you can play with the opacity of your windows. This is done by putting your mouse over the window, pressing ALT and scrolling with your mousewheel. Now I wanted to try something different, I wanted all my windows, menus, popups, dialogs and tooltips to be transparent by default. This can easily be done with tweaking compiz in the CompizConfig settings manager. For your desktop to be useable, I suggest to use a very dark theme with light icons and a rather clean wallpaper. So in this tutorial I will explain how to get a completely transparent Linux Desktop.

So if you want to try this out, follow this recipe:

The GTK-theme I used is called Mythos from GNOME-look.org. As you can see it's very dark, but that's what we're looking for with transparent windows.

The icon theme I used is called allgrey, again from GNOME-look.org. It's great for dark themes.

Now for compiz, open
System > Preferences > CompizConfig Settings Manager

choose 'General Options' on top of the right pane.

and then in the 'opacity settings' we will have to add entries to all the window types we want.

I suggest to add entries for the following windowtypes:
DropdownMenu (for the main menu), normal (for application windows), dialog, menu , popupmenu, tooltip, notification, utility. With my setup/theme I found that a value of 90 for opacity works best.

With those settings there is only one problem: when watching a video or playing a game, the screen was also transparent. So we need to add an entry for every application that we don't want to be transparent. For example, I didn't want Totem to be transparent, so I created a new entry. Now there are 2 ways of doing this, or we know the name of the application window, so we click on the 'plus' icon and enter the name of the application in the 'value' field, or we can grab it using the 'grab' button. It's important that these overrides should be on top of the list, above the 'normal' entry.
The same thing should be done for 'name=gnome-screensaver', so that the screensaver will not be transparent.

To learn more about this, visit this link

(the emerald theme used in the screenshots is Blackminial. With snap as font and a slightly enlarged titlebar)

EXTRA:
You can also use compiz for your system bell (you know, when you make an error or you want to backup when at the beginning of a line etc). For example you can make your window shiver. This setting is found in the 'wobbly windows' setting. Just enable the 'shiver' option. Now you can disable your audible system bell which is a system beep by default. You'll find this in System > Preferences > Sound , where you disable both system beeps.