Only addons that use the Blizzard addon configuration interface will appear in that list. nUI does not, currently, use it... so nUI will not appear in that list unless you have installed the optional GUI plugin for nUI. I can't speak for the other mods.
My advice is to do a clean install and only install the mods you *know* you need until you've had a chance to use nUI a bit and see what it does for you and what you're missing. Doing a clean install usually fixes most of these kinds of odd problems.
See this FAQ:
http://www.wowinterface.com/forums/s...ad.php?t=21716