After Bobby's death, Dean decided to keep Bobby's flask to remember him. It made its first appearance in Adventures in Babysitting where Dean is keeping it in his bag. It made a later appearance in The Slice Girls where Sam notices Dean drinking from the flask. Sam attempts to talk to Dean about it, but Dean tells Sam he's honoring Bobby's memory with it. Later on, Dean accidentally leaves the flask at Lydia's and goes back for it. Dean tells her the flask means a lot to him.
The flask began take on a bigger role when Garth noticed that the flask was giving off EMF. Garth mentions to Dean that the flask might mean that Bobby is haunting them. To further his point, Garth uses his EMF meter to show it giving off EMF. It is later revealed that Bobby is in fact tied to the flask, but unseen to Sam and Dean. Dean realizes he left the flask and goes back and gets it.
It is soon revealed that the ghost of Bobby Singer is tied to the flask, but Sam and Dean are unaware of this fact. They soon become aware that Bobby is tied to the Flask in Of Grave Importance. In order to investigate a haunted house on his own, Bobby removes the flask from Dean's coat pocket so he can look around the Van Ness house. The flask goes back into Dean's possession once Dean returns to the house, only to find a ghost Bobby. A bit upset, Dean puts the flask in the back of the car.
In The Girl With The Dungeons and Dragons Tattoo Dean still has the flask and is using it. When they recruit a hacker named Charlie for help, Bobby puts the flask in her bag. Charlie finds the flask and calls it a good luck charm while drinking from it. Dean tells her not to loose it due to it being a family heirloom. After the job is done, Dean gets the flask back.
In There Will Be Blood, Dean locks it in a safe, because he and Sam fear that the more violence Bobby takes part in, the closer to a vengeful spirit he becomes. However, he possess as housekeeper and cracks the code to the safe, taking the flask with him as he leaves, still in the woman's body.
In the Season 7 Finale Survival of the Fittest, Sam and Dean burn Bobby's flask on Bobby's request, after he realizes how dangerous he is. As Bobby's flask melts, Bobby's ghost is finally laid to rest.