Roro requested a tutorial on transparent backgrounds. To have your icon always match the background of the SS layout, no matter what colour, for example:
Program used: Photoshop CS3, extended version, but is definitely translatable.
Example icon: 
Whatever icon you're making, if you're using an image or text or brushes, if you want to have a transparent background, you simply do not create a background layer with a colour. Leave it blank, when you merge layers you should merge them as "visible" and not to "flatten" them as this will give you a coloured background.
Your layers should look like this:
And when you save them, a JPEG or GIF image will give you an automatic background, so you must always save as a PNG-24 and check the Transparency option, like so: