Well, there was Debby Stark's The Dawning - where Lois quietly knew for a very, very long time.
That story is unfinished though, so you may not want to get started on it until it has a resolution.
One of my personal favourites where Lois gets her revenge is the aptly named...
Lois\'s Revenge . <g> A very funny, steamy and cute vignette. And don't miss its sequel,
Clark\'s Response