While researching performance at Yahoo!, we discovered that moving stylesheets to the document HEAD makes pages load faster. This is because putting stylesheets in the HEAD allows the page to render progressively.
Front-end engineers that care about performance want a page to load progressively; that is, we want the browser to display whatever content it has as soon as possible. This is especially important for pages with a lot of content and for users on slower Internet connections. The importance of giving users visual feedback, such as progress indicators, has been well researched and documented. In our case the HTML page is the progress indicator! When the browser loads the page progressively the header, the navigation bar, the logo at the top, etc. all serve as visual feedback for the user who is waiting for the page. This improves the overall user experience.
The problem with putting stylesheets near the bottom of the document is that it prohibits progressive rendering in many browsers, including Internet Explorer. Browsers block rendering to avoid having to redraw elements of the page if their styles change. The user is stuck viewing a blank white page. Firefox doesn't block rendering, which means when the stylesheet is done loading it's possible elements in the page will have to be redrawn, resulting in the flash of unstyled content problem.
The HTML specification clearly states that stylesheets are to be included in the HEAD of the page: "Unlike A, [LINK] may only appear in the HEAD section of a document, although it may appear any number of times." Neither of the alternatives, the blank white screen or flash of unstyled content, are worth the risk. The optimal solution is to follow the HTML specification and load your stylesheets in the document HEAD.
[Steve Souders is Yahoo!'s Chief Performance Yahoo!. This is one in a series of Best Practices for Speeding Up Your Web Site. This article is based on Steve's book High Performance Web Sites, published by O'Reilly.]