Leon/fallenRogue has a lengthy blog post debunking some criticism on the difficulty of skinning SharePoint, and offers some good tips, one of which is below: In order to make the application (/_layouts/) pages that are part of your SharePoint solution
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Read the complete post at http://feeds.feedburner.com/~r/monotonous-moss/~3/257845753/moss-on-skinning-sharepoint.html