Cal-el aka Clark Kent's Vulnerbilities

Green kryptonite is Clark's most severe and dangerous vulnerability. Green K in any size or form renders Clark powerless and painfully incapacitated; he once remarked that broken ribs hurt less than green K exposure. When Clark is exposed to green K, his veins become dark and prominent, he sweats profusely, his vision blurs, and he clutches his stomach as if nauseated; it is shown that his blood literally appears to boil. He can barely stay on his feet and usually collapses to the ground in agony. Prolonged exposure renders him unconscious and would probably kill him. Clark can draw blood or bruise while in the presence of green K. Since the meteor shower, it is found in abundance in Smallville and Clark has fallen ill or passed out from ingestion, inhalation, and close proximity to green K. Clark's weakness to green kryptonite started at least as early as grade school; however, he did not figure out the connection with the meteor rocks until his teens, saying he is "allergic" to them. Clark and his parents keep a green meteor rock in a lead box in case they ever had to subdue him in an emergency. It has been shown that even a simple layer of lead between Clark and the kryptonite is enough to prevent Clark feeling the effects of kryptonite bullets, while lead paint proves sufficient protection from conventional meteor rocks. While kryptonite weakens Clark's powers, he has been shown to still be able to use his abilities in its presence, although it takes more effort for him to use them (Source episodes: Pilot, Metamorphosis, Leech, Phoenix, Extinction, Obsession, Onyx and Splinter)
Red kryptonite makes Clark lose his inhibitions and social conscience. Similar to the effects of alcohol, Clark becomes Kal, who is unpredictable and belligerent. On red K, Clark is also sexually aggressive (though apparently not sexually active), flirtatious, and unconcerned with keeping his abilities a secret. He is disrespectful, uncaring of others' feelings, and can become violently dangerous. Also, Clark hardly ever swears unless he's under the influence of red K. (Source episodes: Red, Rush, Exodus, Exile, Unsafe and Crimson)
Blue kryptonite strips Clark of his powers, but not painfully-so like green K; simply coming in contact with it appears to merely shut his powers down until he is no longer touching it. (Source episode: Blue)
Black kryptonite can separate or combine Clark from/with his Kryptonian personality, Kal-El. Black K works on humans as well, physically splitting them into their good and evil personas. (Source episodes: Crusade and Onyx)
Silver kryptonite makes Clark extremely paranoid and suspicious of those around him. Silver K's effects on Clark are similar to those of hallucinogenic drugs. His behavior becomes erratic and he sees and hears things that are not there, such as perceiving balance sheets as bills. In addition, Clark manifests physical symptoms such as sweating, labored breathing, and puffy, dilated eyes, although his powers are unaffected. (Source episode: Splinter)

Clark beaten and weakened by green kryptonite beads.

Clark is uninhibited while exposed to red kryptonite.

Clark is split in two by black kryptonite.

Silver kryptonite makes Clark paranoid.
edit Metahumans
[edit] Kryptonite-infected
Although most metahumans received their powers and abilities from green kryptonite, Clark's vulnerability or immunity towards them seems to be random and arbitrary.
Kryptonite vulnerability
Clark could not approach Earl Jenkins due to the kryptonite embedded in his body. (Jitters)
A boy covered in Kryptonite was invisible; his X-ray-vision erratically turned on and off whenever he tried to look at him with X-ray-vision. Also, throughout the episode, Clark was weakened slightly when near the boy, but still had full use of his powers, apparently. (Shimmer)
Clark could not approach Wade Mahaney until his kryptonite tattoo wore off. (Kinetic)
Physical vulnerability
Sean Kelvin rendered him unconscious for several minutes. (Cool)
Clark's powers were leeched by Eric Summers through a lightning strike when in physical contact with kryptonite. (Leech)
Wade Mahaney was able to injure Clark by sticking his hand in Clark's abdomen. (Kinetic)
Tyler Randall wasn't able to turn him to ash, but he did cause him pain with his touch and the skin where Tyler made contact turned black. (Reaper)
Justin Gaines threw him across the room when he used his telekinetic ability on him. (Crush)
Eric Marsh was able to overpower him with his strength, but Clark's other abilities were enough to allow him to turn the tide. (Witness)
Nathan Dean was able to incapacitate him with his screech. (Whisper)
Alicia Baker was able to teleport him. (Obsession)
Mental vulnerability
Cassandra Carver saw his future, and unlike humans he was also able to see her visions when the two of them were in contact. (Hourglass)
Sarah Conroy entered his dreams and kept him asleep, commenting that Clark's mind wasn't like others. (Slumber)
Jordan Cross saw a vision of his future when he touched him. (Hereafter)
Dawn Stiles was able to possess him, but was driven out by Jonathan's use of kryptonite. (Spirit)
Kevin Grady attempted to erase Clark' memory for a few minutes; because Kryptonian physiology is different from humans, Clark had almost total amnesia. (Blank)

Sean steals Clark's body heat.

Clark can see the invisible man with his x-ray vision.

Clark is possessed.
[edit] Others
Clark was vulnerable to Frederick Walden's energy-blasting powers. (Calling)
Clark was vulnerable to Mikhail Mxyzptlk's control of his body. (Jinx)
Clark was incapacitated by Black Canary's sonic scream as it made his ears bleed. (Siren)
Clark was vulnerable to the Orb when it stripped him of his powers. (Arctic)
Clark was vulnerable to Maxima's mind control, and was overcome by desire when she used her powers on him. He was able to break this mind control when he saw Lois. (Instinct)

Mikail trips Clark.
edit Hypnosis
Clark tried to kill Chloe after receiving a mind-altering email from Molly Griggs. (Delete)
Clark did everything he was told after Simone hypnotized him with her blue gemstone. (Hypnotic)

Simone's hypnotic gem.
edit Magic
Main article: Magic
Clark was vulnerable to the magical abilities of Countess Margaret Isobel Thoreaux. (Spell)
Clark's powers can be taken away by magic if the spell and the spell-caster are powerful enough. This was done by Isobel Thoreaux. (Spell)
He was also vulnerable to the two weapons Isobel previously enchanted using a spell. (Sacred)

Clark is vulnerable to magic.
edit Other Vulnerabilities
Clark was blinded by his own heat vision after it was reflected off of a piece of meteor rock that had been refined into a multi-cut stone for use as jewelery. In addition to the loss of sight, the skin around his eyes was red. He also experienced pain when Nathan passed a blow torch across his eyes, but the injury destroyed the scar tissue hindering his sight. (Whisper)
Clark was vulnerable to the Starblade, which he suspected was made of Kryptonian metal. He sustained a severe stab wound from the blade and lost a significant amount of blood before he was healed through the power of Jor-El. (Talisman)
Clark succumbed to the hallucinogenic dreams of an airborne toxin in Scare but unlike everyone else exposed, he was able to recover on his own.

Clark catches a cold-like illness in the Phantom Zone.
While in the Phantom Zone, Clark had no physical invulnerability due to the fact that there was no yellow sun present to empower him, and he was thus able to be punched and scratched by the phantoms. He also returned to Earth with an illness that resembled the human common cold. He experienced fatigue, sneezing, a scratchy throat, and plugged-up ears. (Sneeze)
While Clark was on Krypton in the past (Apocalypse) Clark had no abilities under Krypton's red sun, thus causing him to be easily overpowered and even bleed due to his human level attributes.
Clark is vulnerable to the various intergalactic creatures that have escaped from the Phantom Zone. Repeated punches to the face from General Zod caused Clark to bleed from his mouth. The deadly vines generated by Gloria were able to cut and impale him. Aldar, Titan and Baern were all able to overpower him, and Dr. Hudson was able to enter Clark's mind and keep him in a prolonged hallucination. Baern's radiation blast were powerful enough to knock Clark back and with the force of the blast Clark was blown out of the barn and was stunned for several minutes. Due to his shared DNA with Titan, Wes Keenan was also able to overpower Clark, but did not cause Clark to bleed. Clark later remarked that their blows were the strongest he's ever felt. Bizarro was able to enter Clark's body, extract his DNA, and overpower him. Presumably, Aldar, Dr. Hudson and Bizarro posed greater threats to Clark than the other Zoners, since the Martian Manhunter had to interfere in each case. (Source episodes: Arrival, Vessel, Zod, Wither, Fallout, Static, Labyrinth, Combat, Prototype and Phantom.)
Mikhail Mxyzptlk and Tim Westcott caused Clark to choke, suggesting that he still needs to breathe air. (Jinx, Pariah)
Jor-El can remove Clark's ablities at will, therefore making him vulnerable and essentially human. In this depowered form, Clark can be killed in conventional ways, such as being shot. (Arrival, Mortal, Odyssey)