The Pilot episode of Smallville describes the population as 25,001 in 1989 and 45,001 in 2001. For such a small town, they seem to have an inordinate number of deaths. This article details the body count of each episode in Season Three. Serious injuries and other crimes are also noted, but only actual lives lost will be tallied. Likewise, although Clark saves people from various ill fates, his rescues are only counted if death seemed reasonably certain. Since the death of a metahuman is not always certain, continual updates are expected.
One of the bank robbers in a clown mask appears to open fire on one of the bank patrons huddling on the floor. His death is not portrayed on screen, but its hard to imagine he survived. Lex kills his imaginary friend Louis, but that doesn't count.
Lana kills the thug holding Martha hostage. Lionel's security guard kills the other thug. He appears to kill Morgan Edge as well, but he will reappear in a later episode. Helen Bryce accidentally kills the pilot (while trying to kill Lex), but she gets away, too.
Sarah Conroy appears to die in several dream sequences. Traveler disintegrates, but he wasn't real. Nicholas Conroy was drugging Sarah but it is unknown if he would have killed her. He tried to kill Lana but Clark saved both girls.
Seth Nelson used his magnetic abilities to control Lana. She needed saving (as usual), but she was not in mortal danger. Although Clark did not kill Seth, he did use lethal force against him. Without the dialogue to confirm otherwise, there is no reason to expect Seth to survive the electric shock he was given.
Villain: Incarcerated (Eric); dead (Van); dead (Ian)
The two Ians kill Van. Claire Foster dies in a car accident, but Lionel is suspected. Eric most likely killed Ian. He tries to kill Clark, and Clark tries to save Lex, but Lex survives his treatment without any help.
Clark saves Alicia Baker from a crashing elevator, but she wasn't really in danger. Alicia Baker beats her father badly enough to put him in the hospital with a respirator. She threatens Clark's parents, but never follows through. She tries to kill Lana with a knife, but Clark stops her. Lionel orders Lia Teng to deny Adam Knight his medications, but it will later be revealed that she does not.
Vince Davis dies twice from liver disease. Lia Teng revives him once. Garrett Davis threatens to blow up the Smallville Medical Center unless his brother is given a liver transplant. Clark is able to save the lives of perhaps a hundred people in the hospital. In the end Garrett is shot and killed by a deputy sheriff.
Adam Knight kills Lia Teng and seven other lab technicians. He injures Glen Burton, Jonathan, Chloe, and the warehouse attendant. He tries to kill Lana, but Clark saves her before Adam succumbs to his illness (again).
Lex participated in a dangerous treatment with Lawrence Garner to regain his memory. Clark tries to stop him but is exposed to the same radical treatment. Lex saves Clark who otherwise would have probably drowned in the kryptonite liquid. Dr. Garner goes into a coma when Clark's seizures cause the equipment to explode.
Emily Dinsmore kills the Talon's new owner and her father Pete Dinsmore. She tries to kill Lana with poison gas but Clark arrives in time to save her. Frank Loder beats up Pete to force him to reveal Clark's secret, but Lex arrives and orders him to stop.
Lindsey Harrison flips a car which then explodes, killing at least one person (and more if there were any passengers). She also kills Frank Loder by vaporizing him and his car. Jor-El dissipates Kara, but it is unknown whether he kills her or simply returns her to the interior of the cave wall. Jor-El likely would have choked Jonathan to death with a rope of energy had Clark not entered the cave wall. Lex chokes while drinking brandy and Chloe and Gabe Sullivan appear to be killed when their safe house explodes.
Twenty-eight people died in Season 3.
There are 8 episodes this season where no one died.
By the end of this season, there are 21 total episodes in the entire series where no one died. That's an average of exactly 7 episodes per season.
Clark saved Lana five times12345 and Lex twice12, Pete twice12, Chloe twice12, and Jonathan three times123.
Clark's life was in real mortal jeopardy four times this year: Jonathan saved him from a kryptonite bullet, Pete saved him from falling, Lex saved him from drowning in kryptonite, and Jonathan saved him from a knife wound.
There was only one fatality among the staff of Smallville High: Joseph Altman.