With 40 different schools, wouldn't you have 40 different portals?  Or at least 40 different pages that could have their own skins?

Here's another method that is kind of like your #2 for mixing in dynamic changes with a background style:

http://blogs.snapsis.com/PermaLink,guid,105f8d79-ffbc-4859-836c-b747364fa59c.aspx

Also remember that you can have your 40 different skins in one skin folder and keep the same base CSS (skin.css) with your changes in css files for each skin that matches the skin name

for example skin1.ascx will automatically link in skin1.css

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I know this is an old post but still....
There is a solution for the "school" problem you are mentioning...
Use this in your ascx file:

<div class="<% = PortalSettings.PortalName %> skinselector">
    put the rest of the skin here
</div>

OR

<div class="<% = 'Portal_' & PortalSettings.PortalID %> skinselector">
    put the rest of the skin here
</div>

Now you can use the portalname or the portalId to define spectific CSS for each portal in one CSS file.
There's one problem if you use the portalname, you will have to replace invalid characters and spaces in the portal's name... (with a script in the ascx page) or it will not work.

You could also load an extra CSS file based on the portal's name or ID I think...

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