I don't recall there ever being a thread for the Sopranos while it aired. I watched the series through recently and read a few theories on who killed Tony. All presuming Tony actually died. I remember being shocked at the end. Like everyone I tried to remember what had happened in the last few minutes, who could have done it. Below are the popular theories and my thoughts on why some of them don't fit.
Theory 1: Little Carmine (Lupertazzi) had Butch Deconcini kill Phil (Leotardo) and Tony (Soprano). Little Carmine was the rightful boss of the Lupertazzi family but was outstead by Johnny Sacromoni and then Phil Leotardo. Problem here is Little Carmine had always got on well with Tony and had no reason to kill him, in fact Tony was one of the few mobsters who would have been happy to see Little Carmine as boss as Little Carmine was easily manipulated.
Theory 2: Butch Deconcini had Tony killed to see through Phil's (Leotardo) plan of killing off the leadership of Jersey so the Lupertazzi family (under Butchie) could take over what was left of the Jersey crew once the Soprano's were gone. The problem with this theory is that it doesn't end the war. Butch already gave Tony the go ahead to kill off Phil and he was keen to make peace, he already had a lot on his plate not being killed himself for betraying Phil without having to worry about reprisals for killing Tony too.
Theory 3: Patsy Parisi: Tony had Patsy's twin brother killed early in the show and Patsy had tried to kill Tony at his house, but bottled out. Patsy was definitely a killer and was scared his son (Jason) was following him into the Soprano crew and mob life. Jason Parisi was good friends with Jason Gervasi who was in turn the son of Soprano crew member Carlo Gervasi, who had flipped to the FBI. The problem with this theory is Patsy would have been painting a target on his own back and put his family in danger. To wait this long to take another shot at Tony doesn't make much sense.
Theory 4: Eugene Pontecorvo's Brother: In the first episode of the last season 'Members Only' Eugene inherits $2m. He and his wife plan to move to Florida and he seeks permission from Tony to leave the Mob. After some pondering Tony refuses, which is told to Eugene through Sil. Eugene is distraught and takes his own life, presumably wanting a better life for his family but thinking his wife and kids will never be able to leave while he is connected to the Jersey crew. 3 o'clock: When Christopher is shot and coming out of his coma he tells Paulie and Tony of his near death experience and gives them a warning from dead associate 'Mikey Palmice.' The warning is 3 o'clock. In the final scene we see a man sitting at the counter wearing, the same members only jacket Eugene Pontecorvo was wearing in the first episode of the season. Later in the scene the man goes into the men's room, which is situated at Tony's right hand side, at 3 o'clock.
Spoiler for Last scene: