Back in the 1990s just before and during the Superman Death (thanks to Doomsday) and rebirth, Lex's "son" was in charge of LuthorCorp, but there was a catch. Back in the day, Luthor was in the habit of wearing a Kryptonite ring, believing that the substance was only harmful to Kryptonians. Unfortunately, long-term exposure proves fatal to humans as well. As we all know, Lex is never without a Plan B and so, faked his death in a car accident, then had his brain and eyes removed from his original body and placed in a cloned body. Of course, the close was much, much younger than the aging Lex of the comics and, to combat his original baldness, he grew a full head of long, red hair and a beard. He pretended to be a much nicer guy than his "father" but he was still the same old Lex inside.
In Smallville season 8, Oliver Queen admits to killing Lex in an explosion because he was far too dangerous to Clark and to the rest of the world while still alive. Explosions (at least on TV and in the movies) are poor ways to make sure a person is dead because their body is (supposedly) blown into little, tiny bits and there's no real proof they didn't somehow escape at the last second. Assuming Lex didn't escape and he really did get blown up, he could have previously made arrangements that, in the event of his death, he should be cloned. His "personality" could have been preserved in typical science fiction fashion, so a "true" representation of Lex could be recreated to get his revenge against first Oliver for killing him and then against Clark for the many and varied "sins" Lex imagines Clark committed against him.
One scene briefly shown in the season 10 trailer was a sequence involving Lionel Luthor. As we saw in season 7, Lionel was murdered by Lex (he was on a killing spree that week) when Lex pushed him out of his office window at LexCorp. There was no way Lionel could have survived the fall. Lex positively IDed the body and there was no chance to make a sudden switch in mid air. But wait.
Cloning technology. Lionel was aware that Lex had cloned Julian and Lionel watched the Julian clone die right in front of him (in a murder ordered by Lex). Lionel, for all the changes he may have gone through as a result of being Jor-El's vessel, was still Lionel. He was quite capable of locating Lex's cloning lab. What if he donated some of his DNA to the cause?
Question: Is the Lionel who comes back in season 10 a clone, or did Lionel have himself cloned as a precaution much earlier, so that the murdered Lionel was the clone? In the latter case, it would mean (or could mean, depending on how many Lionel clones are around) that the original comes back, perhaps for a showdown with the Lex clone. As Jor-El's vessel, he might also return to assist in Clark's final transition to Superman.
The whole cloning thing opens up a veritable can of worms (and their clones) since you can bring back just about anyone if you had some of their DNA and a way to record their original personality and memories (this has been done just a ton of times in films, TV, and comic books). No matter who may have been killed, they could return, just to mess with everyone's head.
We know Jonathan Kent returns. Is he a ghost, a flashback, a vision in Clark's near-death experience...or a clone? If a clone, just how will Clark and particularly Martha handle it?
The only Lana clone we're aware of is one that was never given life, but if more genetic material remained, other Lana clones could be constructed. If Lana shows up in Smallville or Metropolis, who's to say if she's "live or if she's memorex". Even people who haven't died or disappeared could be cloned. Kidnap and imprison the originals, and then program the clones to do your bidding. At that point, anything's possible. Smallville could become another remake of Invasion of the Body Snatchers.
This plot line could either be wonderfully creepy or totally ridiculous, but I'm hoping for the former. Now, without further ado, please send in the clones.
Addendum: Oh duh. I completely forgot about the Cadmus Project. If anyone's into cloning...it's Cadmus.