Well, for instance in the StopDesign theme, at the bottom of the page there are links (RSS, Archive View, Powered By. . .) but on my edited template, the links (and indeed text) aren't clickable.
The links are in the code but when the page is rendered then the links are no longer links.
I would guess that the answer lies in the DIV tages I have at the bottom that is somehow stopping it render the links as links.
It's strange though as the text itself shows the right color for a link, but isn't actually read as a link :S