There's a lot of information in the MS KB article,
How to modify your folder view settings or to customize a folder that you already know but there are a couple of things in there you can try.
Look under the sub-heading, "Manually create a folder picture," for the way to change the appearance of system folders that do not have the Customize option.
Look under the subheading, "Troubleshooting," for the registry edit that allows Windows to remember the settings for more than the default 400.
That article may give you some clues about applying a customized folder appearance globally. So far, I haven't found a way to do that if "Apply to all folders" doesn't work.