UPDATE: I've gotten so many emails, tweets and comments below expressing confusion about how Jesse figured out about the cigarette swap that I decided to simply lay out the chronology as follows:
1)In "End Times," to get Jesse back on his side in the war against Gus, Walt arranges for Huell to steal the cigarette pack with the ricin cigarette out of Jesse's pocket and replace it with a different pack. Saul calls Jesse to his office on shaky reasons, and Huell pats him down in a way that gets Jesse's attention. Walt doesn't use the ricin to poison Brock, but rather a lily of the valley plant that will have a similar but less dangerous effect on the boy.
2)When Jesse hears that Brock has been poisoned, he realizes that the ricin cigarette is missing, then (correctly) puts two and two together that Huell stole it, on Walt's orders. He storms into Walt's house and threatens to kill him for poisoning Brock; Walt convinces Jesse that it was Gus, not him, who wanted to hurt the boy — specifically so Jesse would come to this conclusion and murder Walt for him — and that Tyrus must have lifted the cigarettes from Jesse's locker at the Super Lab. Jesse accepts that Mr. White would never hurt a child, whereas Gus has a history of hurting children, and lets go of the theory about Huell.
3)Doctors later figure out that Brock was poisoned by a lily of the valley, not ricin, making Jesse doubt Walt's theory about Gus manipulating Jesse into shooting Walt, and leaving him to wonder what really happened to the ricin cigarette. Walt stages a phony search of Jesse's house and plants a fake cigarette (containing salt, not ricin) inside Jesse's Roomba. None of this sits well with Jesse, but he once again believes Mr. White.
4)Over the course of season 5, starting around the murder of Drew Sharp, Jesse has begun to realize that he shouldn't believe anything Walt says. Walt claims to be broken up over Drew's death, then whistles while he works. Walt claims that Mike left town alive, when Jesse knows that Walt would've never taken out Mike's guys unless Mike was dead. Walt gives Jesse a whole song and dance about how leaving town will be good for Jesse, when Jesse knows that it will be even better for Walt.
5)Having been primed to disbelieve any word out of Walt's mouth, Jesse goes to Saul's office, lights up a joint and gets scolded by Saul, who knows his relocation expert won't pick up anyone who's high. Saul orders Huell to again pick Jesse's pocket to get rid of the marijuana.
6)At the pick-up spot, a nervous Jesse reaches for his pot, and can't find it. He frantically checks all his pockets, but all he finds is a cigarette pack. Staring at the cigarette pack, and realizing Huell dipped into his pocket without him noticing, Jesse realizes that his first suspicions about the ricin cigarette were correct, and that Mr. White was manipulating him into turning against Gus, endangering Brock's life in the process.
That the ricin wasn't actually used on Brock is beside the point. Jesse knew from the beginning that Huell had picked his pocket, and that he must have done it on Mr. White's orders. He has been thinking about this often in the months since it happened — far more often and more intensely than those of us watching the show have, and in a more compressed time period. When he realizes Huell picked his pocket, and stares at another crumpled cigarette pack, everything clicks into place about the events of "End Times" — including how convenient it was that this terrible thing happened to Brock, which turned Jesse back into Walt's ally, at the exact moment Walt needed an ally against Gus — and he goes on the warpath against Saul, Huell and that ******* Mr. White.
You may disagree with whether Jesse would have put all the pieces together like that, but that's what happened.
Read more at Review: Breaking Bad - Confessions: Master thespian