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.
Annette O'Toole's final appearance as a series regular. (She would return in the three final season episodes.)
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.
Lois gets a location for Lex's secret project from Wes. The location is 38°32'N 95°32'W. The location is some 22 miles southwest of Topeka, Kansas - pretty much in the middle of nowhere, and nowhere near a river or any other body of water.
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.