Some great Smallville fanfics I've read

Never Quite by aforgottenwish

"It was too close," he repeated, yelling this time. "Too close to Lex and to Lana. It was too goddamned close to that laboratory; I could still smell the blood and fire, I could still hear the wind whistling through the holes I'd punched in the walls and squeaking as it blew through the equipment that they tied me to."

This is sort of weird/different, but still so captivating. Sadly, it appears to have been completely abandoned by the author. It's only a few chapters long so far. 

This is actually a sequel to another story called Antipathy, but that story is so incredibly brutal that I don't recommend it. I actually had nightmares afterwards about having my chest cut open... lol. I'm sensitive.

In Antipathy, Clark gets outed, kidnapped and tortured by Lex, and after endless sufferings Lex experiments with different types of kryptonite on him. When he tries the black type, Clark's Kryptonian side takes over, and he brutally murders all of the scientists and Lex... ouch. (Black kryptonite should technically split him into two separate people, but whatever. I can ignore that.)

In this one, the sequel, you find Clark - now almost a complete different person - living in Africa with a new identity as Kaleb Elliot. And that's what makes me like this story so much. Clark hasn't just lost his memories and become a different person, he's just switched personalities. Not like when he's on red K, but like a more human variation of Kal-El from the episode "Crusade". He has left his old life behind to deal with the emotional scars the torture and experiments left him with. But some events forces him to go back and revisit his old life and bad memories.

This is so well written! The language flows so well, and I got really fascinated by Kaleb.

I am a huge fan of the regular Clark, but this new character is so complex and fascinating that "Never Quite" gets first place on my list. Old Clark doesn't come back! That's what makes this story so original.

Smallville Armageddon Aftermath by IolantheAlias

Yet another sequel. This is actually a sequel by a different author than the original, but this turned out to be my favourite of the two. 

The first story, "Armageddon" is a different take on the Smallville episode "Apocalypse". Clark gets sent to another world where he never existed, and Zod has taken over the world and killed most of the human population. His old friends are now members of the resistance, and when they figure out that he is part of the same species who killed all the humans, they quickly take him prisoner. He eventually manages to convince them that he wants to help, and helps them stop Zod in the end of the story, and gets sent back to his own universe.

"Aftermath" however, tweaks the ending to "Armageddon" a bit, so that Clark stays in the alternate universe. It starts with Clarks trial, where the others discuss what they should do with him. He ends up getting the job of bodyguard for the parallel version of his mother, who hates him with a passion. But during the story, they gradually become friends, and that's what makes this story so good. The realistic progress in Clark and Martha's relationship. It actually takes some time for her to trust him.

I really like this one, and it updates somewhat regularly. 

One downside is that it recently started introducing classic Superman elements like the glasses and the suit. This is just a personal dislike. I always felt that this feels unnatural and out of place in the Smallville universe. But I love this story so much that I'll try to overlook it for a bit longer.

SmallvilleX: Evolution by ben10987654321

This is a crossover between X-men: Evolution and Smallville. Clark gets recruited to "Xavier's school for the gifted", but catches the attention of Magneto at the same time. He gradually makes friends, gets a girlfriend among the mutants and gradually evolves his powers. I think this is set sometime in the earliest seasons.

I've got some problems with the way it's written (in the present tense, "Clark stands at the entrance to the farm leaning against the post."), and it's a bit slow paced, but I love it anyway. Especially the latest chapters.

Honorable mentions:

• Blind Trust by htbthomas – A short, but very nice story. I love how Lois figures out that Oliver knows the Blur, and how Lois have a blindfolded meeting with Clark as the Blur. I usually like stories with a bit more plot and action, but this one just warmed my heart. It could have been better if Clark wasn't revealed at the end, but it's okay.
• Lèse Majesté by ancarett – It's a decent story, but I love it simply for something Chloe says to Oliver in the second part of the first chapter, when Oliver is annoyed with Clark's line of reasoning: "Welcome to the Clark Kent show. He'll either drive you mad or you'll learn to work around it."