Within Temptation and and Nightwish are a few of my top favs as well...
some others:
Theatre of Tragedy (both old and new singer are good but I prefer their older stuff)
Sirenia (Switched front singers too but both are very good. Love their stuff)
Epica (bit to opera for me but when Im in the mood, its nice)
EdenBridge (similar to Nightwish IMO)
Leaves' Eyes
Draconian
As far as I know all the bands listed have clean lyrics. Not sure about Epica I don't listen to their stuff too often but the rest are pretty decent. THeatre of Tragedy had a nude lady on the cover of one of their albums and their older stuff is a bit darker than the rest listed but I don't think I've come across anything real objectional in their lyrics.
Within Temptation isn't Christian as far as I know but they're clean (some of their lyrics speak of mother earth and theres even a song about mother earth but its not really bad. Really just a song about nature)