During the fight with Clark, the Phantom Wraith takes some of Clark's DNA to become "evil Clark". This is Smallville's version of Bizarro, a result of a long ago Kryptonian experiment as explained by the Martian Manhunter. In the comics, one version of Bizarro was a laboratory-created evil Superman clone where another was an alternate reality Superman from a Bizarro World.
In "Lineage" Clark wonders if he even has DNA. In this, it is proven that he does, as Bizarro uses it to copy Clark's form to create a host for itself.
On the Season 6 DVD box set, a deleted scene gives more insight into Lana and Lionel's deal. Lana secretly meets with Lionel to give him the DVD featuring the wraith, saying she's fulfilled her half of the bargain. Lionel informs her that her role isn't finished, but Lana declares her intention to leave Lex. Lionel tries to remind her that they are doing this to protect Clark, and that she must stay with Lex a little longer, but she is reluctant to believe him since he threatened to kill Clark. Lana revelas how terrified she is, but seems to agree when Lionel assures her she is helping Clark and the world.
The conversation between Clark and Martian Manhunter is very similar to the conversation that they had in a deleted scene in "Labyrinth." Presumably the writers originally intended for the Manhunter to explain his backstory to Clark halfway through season six, but when the scene was deleted from "Labyrinth" they moved the conversation to the season finale, "Phantom."
This episode marks the second time Clark has nearly killed someone he blames for the death of a girlfriend. The first time was in "Pariah" when he attempted to strangle Tim Westcott for murdering Alicia Baker. Interestingly, he appears to have been much more willing to kill Westcott, than Lex, and does not seek an explanation from him.