If you're talking about Links SQL 2.x, then it would require writing code to do it. For Gossamer Links 3.x, it's somewhat easy to do:
Since the order is based on the order that they're in in the category loop, you can either do the reordering in the templates (you could loop through the category list twice and only print odd categories the first time and then even ones the second time), or do that reordering in the code (write a global that uses the category loop, reorders it, and then returns a new array).
The first way would be something like this:
Code:
<%loop category_loop%>
<%~if even%><%nextloop%><%endif%>
<%~if row_num == 1%><dl><%endif%>
<%include subcategory.html%>
<%~if row_num == $category_loop.length or row_num == $category_loop.length - 1%></dl><%endif%>
<%endloop%>
<%loop category_loop%>
<%~if odd%><%nextloop%><%endif%>
<%~if row_num == 2%><dl><%endif%>
<%include subcategory.html%>
<%~if row_num == $category_loop.length or row_num == $category_loop.length - 1%></dl><%endif%>
<%endloop%>
Adrian