Melancholy of Suzumiya Haruhi is only the first of 7 or 8 stories about Suzumiya Haruhi. A sequel wont be unexpected.
I'm not sure about GTO, the manga goes further and alot of stuff happens before but I think they've covered the best parts.
The Twelve Kingoms hasn't been finished yet (the novels) I think, so they cant continue the anime, which is a damn shame.
FLCL is not the kind of story that lends well for a sequel .. I mean, look at what they did/are doing to Neon Genesis.
Hikaru no Go could use a continuation and Hajime no Ippo.
Most of the newer series (such as Suzumiya and Back Lagoon) are basically made to have sequels. It probably easier (and more profitable) for the anime companies.
--Jarudin--