Available in the (streams) dev branch now: Custom icon colours for your system apps.
To use, visit your installed apps page and select "manage apps". Click on the pencil (edit) button for the desired app.
Look at the icon field. In the case of system apps it will show "icon:something" where "something" varies by app.
Add a space after this and type "_red" and submit. This app icon will now be red.
You can use any of the 16 predefined browser colours. Just add an underscore to the beginning.
aqua, black, blue, fuchsia, gray (or grey), green, lime, maroon, navy, olive, purple, red, silver, teal, white, and yellow
Issues: This will not work on personal apps which use a url for the app icon, as these are already shown in full colour; only for system apps that contain "icon:" in the icon description.