Littlefinger and Ollena pretty well admit to having done it. Littlefinger gets the disgraced knight who's now the jester to give Sansa a necklace allegedly from his mother. At the wedding Olenna is talking to Sansa while toying with the necklace. We later learn one of the crystals is missing after that and the crystals have traces of the poison in it. While Joffrey is belittling Tyrion his glass is in front of Olenna. Next time he drinks out of it he dies. Littlefinger leaves the necklace on the jester's body to frame Sansa, whereupon they find the evidence.
Littlefinger admits to organizing the thing. In Marjorie's conversation with Olenna she clearly didn't know it was going to happen while Olenna did.
Edit to add: they were doves not pigeons that Joffrey cleaved in half. Also I wouldn't really call it merely a theory that the Frey boys were in Walder's pie. Arya made that point fairly clear. It was also an allusion to the Rat Cook and the price of violating the sanctity of guest right.
Let's talk about this theory. Of course the masses of fans have gravitated towards this but when you look at it closely it is clear that these people look at the facts superficially and haven't really tried to think it through too deeply.
First of all - I do agree that Petyr Baelish is very much involved and said as much in his speech to Sansa boarding the boat. He obviously was involved in getting Sansa away from the wedding and the city, and coordinated the jester's actions. He planned the acts, made the phony necklace, instructed the jester to approach Sansa, get her trust and use the "priceless" necklace as a tool to get her trust (which was a fake made of glass demonstrated by Petyr smashing it with the butt of his knife), and Baelish had to know that the murder was going to happen. But Baelish never once suggested the necklace contained poison or was used in the murder of the King.
In addition Baelish alludes to the fact that he controlled the jester and manipulated him into doing this deed for him, but if you listen closely to his speech on the boat with Sansa in the cabin in the same breath he also alludes that he contols a "great many people". But we all know he does not and cannot control the Tyrells. There is no way that he manipulates them.
Who can he control and manipulate though? The deviants he has served, who have secrets that he sees through his peepholes while they keep the company of his women. People like Grand Maester Pycell who many episodes earlier, while with a courtesan, showed the depth of Grand Maester Pycell's charade of a persona to the world, when Roz left the room and then all of a sudden this old, feeble, coughing withering man jumped up, did some calisthenics, stretched himself up and demonstrated himself to be a far more healthy, spry man than what he demonstrates to the rest of the world - before getting back into the charade when he opens the door and leaves the room.
The necklace being involved in the poisoning is a red herring. There is no evidence - other than that of Grand Meister Pycell's shockingly false testimony throughout the falacious farce of a trial used for the framing of Tyrion - that the necklace had anything to do with poisoning Joffrey.
Everybody buying this theory suggests that the missing stone was plucked off by Olenna and used to poison Joffrey. But why?!?! If Olenna wanted to poison Joffrey why would you go through the whole massive and incredibly, almost impossibly orchestrated and choreagraphed charade with a player (Sansa) who wasn't at all a part of the conspiracy? So that the loose stone might fall off before Olenna could pluck it off? So Sansa could catch her plucking off the stone and unwittingly thwart the assassination of the King? So Olenna might not be able to perform the sleight of hand needed to acquire the poisoned stone and continued on with no one seeing her - in front of the King's guard standing behind Joffrey's and Marjorie's table - and somehow place the poison in Joffrey's cup in front of the world watching?
And do you think they used mind control to somehow puppeteer both Joffrey and Tyrion into their whole standoff so that things would play out exactly how they wanted it too, so that the poisoning occurred exactly when Tyrion held the wine cup?!?!?
Do you know how incredibly non-sensical that all sounds? If Olenna wanted to have Joffrey poisoned - and she was going to do it herself - why wouldn't she just acquire the poison before hand and bring it to the wedding in her pocket? Better yet answer this question...why would Olenna even poison the King herself?!?!? Wouldn't you think that these people in high power don't have their minions doing their dirty work for them? Never mind that Olenna never got close to King Joffrey or his wine during that entire episode.
The only people that got close to Joffrey in that entire episode were Tyrion and Marjorie. And the only time that either of those two even came close to performing an action that could even be remotely close to being considered invasive is when Marjorie fed Joffrey a bite of the pigeon pie or when Tyrion gave Joffrey the cup of wine - which had just moments earlier fallen and bounced around on the floor - there's no way that any poison crystal that was in the cup was still there after it fell.
And yes, it was pigeon pie, not dove pie. Pigeon pie is traditional for the Westeros elite as well as a favorite dish at weddings. Pigeon pie at the purple wedding is referred to many times in later episodes including at Tyrion's trial.
A pigeon pie that came from the kitchen. A kitchen that Cersei earlier banished Grand Meister Pycell too. A Grand Meister Pycell that possesses all the poisons that one could possibly imagine. A Grand Meister Pycell who had motive to frame Tyrion - with his lies in the trial, and who presented the necklace red-herring evidence, and who also had motive to bring pain and punishment Cersei.
We don't know that Joffrey died from "the Strangler" except because Grand Maester Pycell tells us this. What we DO know when you rewatch the scene where Joffrey dies is that Joffrey shows no ill effects from his wine drinking initially. But when Joffrey starts eating the pigeon pie he starts complaining that "this pigeon pie is dry...give me some wine"...and then he starts choking.
And then he's choking more...and then he tries to drink more wine to wash it down.
But why would the writers even have Joffrey bite the pie and then make him say the line "this pie is dry"...just so that he can have a drink of wine?!?! He's at a wedding. He's been drinking wine all day. And we would have expected him to drink wine as part of his meal. Or making a toast. Or just to enjoy himself. The line was unneeded and unnecessary...unless it was a very big hint.
He was choking after he had some pie and before he drank that last cup of wine which Tyrion gave to Joffrey. From a bottle and a cup that neither Olenna - nor anyone else had access too other than Marjorie or the servers - because it was on the King's own separate table.
I like the Grand Maester Pycell theory far more.
And why? Because we always learn the truth at a trial. And at Tyrion's trial the writers all but told us this is exactly what happened...
Tywin: "Did you kill King Joffrey?"
Tyrion: "No."
Tywin: "Did your wife lady Sansa?"
Tyrion: "Not that I know of"
Tywin: "So how would you say he died then?"
Tyrion: jokingly..."He choked on his pigeon pie"
Tywin: angrily... "So do you blame the bakers ..."
Tyrion: ..."or the pigeons...just leave me out of it"
The writers outright gift wrapped it for us. But no one is paying attention.
And then when you watch Grand Maester Pycell's testimony everything he says is a lie because he blames everything on Tyrion - which we all know Tyrion had nothing to do with.
So how does Grand Maester Pycell link up to Petyr Baelish? Because Petyr knows everything about the deviant including all the stories and tales that Pycell tells his women like Roz when they think they are in the safety of secrecy.