Contrary to popular belief some interesting research on page source order has concluded that screen reader and text browser users prefer to see a sites main navigation before the main content.
There appears to be little evidence to support the view that screen reader users would prefer to have the content presented first, or find sites easier to use when this occurs.
On the subject of "skip links" the conclusion drawn was that many of the screen reader options available to more experienced users meant that skip links were much less of a necessity. But the research did indicate that novice users found the skip links a userful device for moving to specific sections of the web page. The conclusion was reached that "websites should continue to provide skip links at the top of pages".
The most interesting item I discovered in the article was regarding "structural labels". The article puts forward evidence to demonstrate that screen reader users find the structure of a page difficult to comprehend and items such as footers for example, even semantically marked up as a list, are often confusing. The solution put forward is to use structural labels to indentify areas of the page as navigation, footer, header, etc. These structural labels in HTML terms would be heading tags that would be hidden using CSS so as not to effect the pages' visual presentation.