Since Supernatural deals so much with family, a lot of the dramatic meat of the show comes from the tension between the characters who are part of that family. Right at the forefront of that are Sam and Dean Winchester, whose constant lies to one another, severe co-dependence, and good intentions often lead to one betraying the other, with Dean doing this to Sam, many times.
Whether it be through hurtful lies and deceptions or by believing he knows better and so imposing his will on Sam's life, Dean so often betrays the younger brother who he is so desperate to protect and look out for throughout the 15 seasons.
When He Used Amelia
When it looked time for Sam to hunt down Benny along with Martin, Dean would not let them do so and used Amelia to drive Sam away to allow him to deal with the situation.
Hacking into Sam's phone and sending a distress signal as Amelia, Dean used the woman Sam still seemingly loved to try and help Benny. While fans do not blame Dean for this - in fact, most think Sam was out of line during the whole Benny story - this minor betrayal hurt Sam.
When He Killed Amy Pond
When Dean killed Sam's friend, Amy Pond, a lot of fans understood why. Monsters were only really evil if they killed humans, and so when Amy started doing so, many fans got it when Dean went behind Sam's back and killed her, despite her promises not to do so again.
Sam, when he first found out, could not understand this at all. He felt incredibly betrayed by his older brother, who not only killed Sam's friend (with whom he also used to have a romantic connection when they were teens), but lied to him about it and kept it hidden as best he could.
When He Lied About What John Said To Him About Sam
"In My Time Of Dying" is not only a fantastic episode named after a Led Zeppelin song, but one of the most important in the show's run, as it sees the death of John Winchester, the introduction of Winchester's taking up a demon deal, and a secret about Sammy.
Despite telling Sam for a long time that John did not have any last words for Dean, the older Winchester eventually caved and revealed the truth. "He said I might have to kill you, Sammy" is a heartbreaking early quote in the show, and Sam was deeply hurt not only by the revelation itself but by Dean hiding it for so long.
His Treatment Of Jack
For the most part, Dean is likable throughout Supernatural. He's troubled with a slew of issues and many bad moments, but still loved. Perhaps his worst point, though, was in his early treatment of Jack.
The biggest example is when he told Jack he would kill him, unprovoked, refusing to really give him a chance, something that hurt Sam. Sam trusted and relied on his big brother and expected better from him in the situation, especially given how good he was to Sam. While Dean eventually came round to Jack before Jack lost his soul, that early abuse from Dean was unacceptable.
Whenever He Made Sam Feel Like A "Freak"
While Dean was always there for Sam and flat-out refused to let him die or be incredibly hurt, Dean could not protect Sam from Azazel infecting him with demon blood, nor Sam’s eventual addiction to the substance.
However, there were many times throughout that Kripke-era that Dean would make Sam feel like a freak because of the demon blood and the psychic powers, even calling him as much, on occasion. This made Sam feel awful and that he was genuinely a freak, a monster, given that he valued Dean's opinion so much.
Anytime He Gave Up
The respect and love Sam has for Dean is immeasurable; he admired the strength and resiliency of his brother so much and so was profoundly hurt anytime Dean threw in the towel.
This happened a few times, like when Dean accepted that he was going to hell, decided he was bound to die on a random hunt, or when he gave up looking for a solution for the Mark of Cain. Sam refused to give up on his brother and got angry at the fact that Dean did not value himself or his life as much as Sam did.
When He Attempted To Put Jack In The Ma'lak Box
Dean's early treatment of Jack, and the emotional abuse he hurled towards him, was arguably nothing compared to his later treatment during times when he tried to lock him in the Mal'ak box.
Dean, the king of free will and not giving up on family, gave up on Jack because he did not view him in the same way as Sam and Cas. He pretty much forced Sam into being alright with locking Jack away for eternity. Despite Sam's protest and being visibly and painfully uncomfortable with it, Dean refused to budge on it, deeming it the only way, which it was not.
When He Didn't Tell Sam About The Ma'lak Box
The Mal'ak box caused nothing but hurt and drama between the brothers, right from the moment it got introduced, and Dean decided to lie about its creation and purpose.
In another instance of him giving up the fight, Dean decided, with the help of Billie, that the only way to keep Michael at bay away from the planet was to lock himself in the Mal'ak box and go to the deepest depths of the ocean. He kept this hidden from Sam with no real intention of telling him because he did not want to be talked out of it - which he thankfully was, causing one of many, many arguments between the Winchester brothers.
When He Gets Obsessed With Using Jack To Kill Chuck
When Billie reveals that she plans for Jack to be used as a bomb to destroy Chuck, Dean gets firmly on board, hiding it from Sam and being alright with Jack giving his life to end Chuck.
Unlike any level of desire he ever had to take out a villain, Dean became obsessed with killing Chuck to the point where he held a gun to Sam's head, refusing to listen to the truth about Billie's plans, focused solely on killing Jack and Chuck. The fact he was ready to shoot Sam shows just how in the wrong Dean was.
When He Let Gadreel Posess Him
Undoubtedly, Dean's biggest betrayal of Sam, and one of the biggest betrayals on Supernatural, in general, was when Dean tricked Sam into saying yes to Gadreel.
Sam was ready to die, and despite Sam arguably being unappreciative, Dean took away that choice and allowed an angel to possess him, which led to the death of Kevin, Sam's body being used to work for Metatron, and Sam saying that Dean was no longer his brother.