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.
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.