Lex had to be written out of the show because Michael Rosenbaum didn't want to come back. It was forced upon the show to accomodate his departure. I seriously doubt any of the writers wanted to have Lex leave.
I don't think Doomsday will be back for the remainder of Smallville. Doomsday kills Superman in the comic books, and that only occurs after Superman has been Superman for quite some time. Simply put, Smallville's Clark Kent isn't going to become Superman until the end of the season/series, so it's highly unlikely that Doomsday will return.
And, since I'm not nearly as knowledgeable about the DC Universe and these two characters, I'll let wikipedia fill you in
Granny Goodness:
http://en.wikipedia.org/wiki/Granny_Goodness
Darkseid:
http://en.wikipedia.org/wiki/Darkseid