I have gotten som questions on how I make my shelf-icons transparent.
So here is a little walkthrough for those it might concern. Note that this is pre Maya 2011.

I make mine in Photoshop on Windows platform. It should be a similar approach with other applications and OS, but this is the only way I have tested.

Start of by creating the 32x32px icon of your choice. Preferably with no more than 255 colors. Meaning 255 colors and 1 open spot for transparent pixels.
When you’re done, select the pencil tool, set your foreground color to RGB: 0 – 254 -0. Note: 254, not 255. That means it’s almost completely green.
Then draw the pixels you want to be transparent with that color. Remember: Only 0 – 254 – 0 will work.. so, as I said, use the pencil tool.

Here is my icon at 500%.

Then select the whole canvas, at press Shift+Ctrl+C to copy from all the layers, create a new document with default settings. Then paste your clipboard into the new document.

Go to the menu and do the following: Image -> Mode -> Indexed Color… And flatten the layers if you’re prompted. Use these settings:

Then at the Forced: dropdown menu, press Custom… to get this window. With all empty color spots, waiting for you to fill them.

Left click the top left one, and set it’s RGB value to 0 – 254 – 0. This will be your transparency. It should now look like this.

Press OK, and then OK again and you’re done. The rest of the colors will fill in automagically. The reason for inserting the green one first is to force it to be in the top, left corner. As far as I know, it’s the only controllable way it will work.
Now you could have a look at the Color Table (Image -> Mode -> Color Table…) to view what colors you’re using, and if there are any open spots etc. Mine looks like this.

Now, the only thing left to do is saving it out as a *.bmp file. (File -> Save as…)
Choose BMP. Here are the settings I use.

It should now work. Just apply it somewhere in Maya, and the green pixels should be transparent. Here is my new icon at my shelf (at 300% scale), along with some other ones.

There you go. I hope you got something out of this.

Best Regards

Christer Bjørklund