I finally got Internet Explorer to behave properly with respect to the sidebar. By taking all the width properties off the individual blocks and adding instead adding the width to a new surrounding <div>, suddenly IE stops screwing up the first link in every list and sub-list. This means I can get rid of all the <!--[if IE ]><li></li><![endif]--> hacks. Yippee.
Now I just need to work out how to get rid of those annoying single pixel gaps in Gecko.