Using ResEdit to make Transparent Icons
If you have a Mac and use ResEdit (Classic mode only), you can even mask the icon to make it transparent.

Here is a primer.  
Hope it helps.
1. Drag and drop your settings file with the icons on to the SuperRezFlip application.
(You can use Copyright.fc as a sample icon file)
(Once you have done this, you can edit the file in ResEdit.  The icons are the CICN resources so you can create your own within it.  Just number all new icons between 28000 and 28999
2. Open the settings file in ResEdit and locate the icon
82704_75419_0.png
3. Double-click on the cicn icon to open the icons resource
101104_15558_0.png
4. Double-Click on one of the icons to open it in the icon editor.
It will look like this
101104_20242_8.png
What you need to do is create the B & W and Masks for this icon.
5. Drag the Color icon on to the B & W and then on the Mask Icon
101104_20221_7.png
This "should" create the B & W and the Mask however as you see in this instance, the mask is NOT created.
101104_20300_9.png
So, to fix this, drag the B & W icon on to the Mask and it will create the mask
101104_20322_10.png
It is the Mask that creates the transparencies.
Sometimes, depending on the icon, you have to manually edit the mask by filling in some holes so that it properly masks.

You can see the effectiveness of the mask by choosing
82704_80723_6.png
and this will display the icon on a gray, rather than white background
101104_20004_5.png

6. Do this to all of your icons and save the file.
7. Drag and drop it back on to SuperRezFlip to convert it back to a settings type file.

As you should see when you double-click on the new Copyright.fc icon that Ed created and that I have placed a mask to, the icon is now transparent
101104_20537_11.png
Rather than having the white background as was the case before the mask was applied.
101104_20646_0.png