Originally Posted by BusterPorn

By default they com up alphabetically, however, Meta always shows up at the bottom. In your dashboard go to:
Links -> Link Categories
Click Edit on the Link you want to edit
Find the Sort Order Field
You can sort by Name, ID, URL, Rating, Updated, Random and Name Length.

So if you have links to other blogs you can sort them by rating either ascending or descending. This would be the amount of times they were clicked though and not the amount of traffic they sent you. Hope that helps a bit.