*sigh* Yes, they are lists, but there are some things you can't format properly in lists (e.g. button-like highlighting doesn't work as I wish)

big amounts of javascript & Co on private pages. It's not fun to wait 5mins and a dozen minimal reloads just to change a page

highlighting works well in lists, and if you want it to look like theres no space between each item, then just set padding and margin to 0

I don't think anyone really overuses javascript (not that i'm aware of) and a few things are implemented for the sake of enhancement, say you have a menu, and you've positioned it all perfect, now you come up with an idea to make it fixed, then Javascript is required, but the good designer also ensures that the site's basic functionality will not be unhindered by this addition of Javascript

and of course, position:fixed breaks on IE