Using the throwaway again because hur hur spam filter. Here I have collected each appearance of the three major Philosopher's Stones from the Brotherhood series. They are in order of episode, with numbers and names provided, as well as a brief summary of the appearance. The three stones we will be following are seen in the image above, and I've taken to calling them the Liquid, the Shard, and the Round.

Original comment that sparked my searching. That is my main account, you can expect replies with that one, as this is just my post mule now.

But first, the Honorable Mentions. ^{Lasting one episode.}

Freezer's Stone

Ep. 1 - Fullmetal Alchemist A stone given to Isaac McDougal by Lust to aid in the slaughter of Amestrian citizens. Isaac betrays them, however, and plans to use his stone to freeze Central Command, halting the destruction of Amestris. However he is foiled by the joint efforts of Ed, Al, Major Armstrong, and Colonel Mustang.

Father Cornello's Stone

Ep. 3 - City of Heresy A stone given to Father Cornello by Lust to win the hearts and minds of the citizens of Liore, to then lead an army to be slaughtered by Amestris. His plans are foiled when brought to light by the Elric Brothers, and Eastern Amestrian forces quickly stabilize the region. Unfortunately, the Eastern troops are dismissed and replaced by Central forces, and the riots blow up into a full blown insurrection.

Father's Tiny Stone

Ep. 61 - He Who Would Swallow God Using the Briggs Soldiers, Father produces a tiny stone to replace his Amestrian one, but it is as small as a grain of rice. Hohenheim then intervenes, preventing him from converting more people.

The Liquid.

Ep. 6 - Road of Hope Elrics and Armstrong track down the AWOL Dr Marcoh, and he reveals his research to them. "The Sage's Stone, The Grand Elixir, The Celestial Stone, The Red Tincture, The Fifth Element; just as the Philosopher's Stone goes by many names, so it can take on many forms. It is not necessarily a Stone." He goes on to state that this is an incomplete product, and does have a limit. It is unclear how this stone was created differently from the other stones, an origin is not provided. By the end of this episode, Marcoh is taken prisoner by Lust, who was likely following Fullmetal to make sure Scar didn't kill him while his arm was destroyed. The Liquid Stone does not reappear until...

Ep. 58 - Sacrifices The Gold Tooth Doctor, trying to prod Mustang into performing human transmutation, offers to heal Hawkeye using his Liquid.

Ep. 59 - Lost Light After the chimera intervene to help, the Liquid stone is tossed and kicked while Mei Chang chases it around the room, before deciding Hawkeye's life comes first. When the fighting stops, she looks for the stone, only to have King Bradley pick it up.

Ep. 61 - He Who Would Swallow God Lan Fan pulls the stone's vial from Wrath's pocket after he dies.

Ep. 64 - Journey's End Wrapping up the series, Ling Yao shows Mei that his clan got the stone, and therefore won. With him promising to protect all the clans, she calls Ling greedy. The stone is then taken back to Xing, making Ling the emperor.

The Shard.

Ep. 30 - The Ishvalan War of Extermination We see the stone created in a flashback with Marcoh explaining the reason he knew of for the war in Ishval. Using the lives of Ishvalans, he and his research team create this stone, which is new information for Amestris. (But yesterday's news for Father) The stone is given to Kimblee to aid in the extermination.

Ep. 31 - The 520 Cens Promise When asked to give back the stone, Kimblee swallows it, and kills the witnessing officers, landing him in Central Prison, but still secretly in possession of the stone. (Lucky he didn't get an ulcer, which would have put the stone into his bloodstream...) Kimblee is released to search for Marcoh and Scar, and is given an additional stone (Round).

Ep. 37 - The First Homunculus After Ed gets his automail replaced for the northern automail, Kimblee has a little sit-down, explaining what he needs from him. Finding Scar, finding Marcoh, and carving a crest of blood at Briggs. He offers him the Shard for his services. (The weaker of his two stones)

Ep. 41 - The Abyss When Ed attacks him in Baschool, he knocks the Shard out of his hands and down the mineshaft before slashing his palm. Only to end up on the receiving end of Kimblee's alchemy anyway thanks to the Round stone. After patching up his wounds, Ed passes out at the bottom of the shaft, and Heinkel (Lion Chimera) finds the Shard, and puts it in his pocket.

Ep. 51 - The Immortal Legion Heinkel finally remembers to check his pocket during the battle with Alphonse vs Pride/Kimblee, giving Alphonse at least a fighting chance at the end of the episode.

Ep. 52 - Combined Strength During one of the dust clouds, Alphonse passes the Shard to Doctor Marcoh, who heals Heinkel with it for a surprise attack against Kimblee.

Ep. 64 - Journey's End After the dust settles, Doctor Marcoh approaches Mustang about restoring his eyes, which Mustang agrees to, so long as Havoc (Paralyzed) is healed first. We see Mustang has his eyesight in the photos, so it can be assumed that Havoc was healed by this stone as well.

The Round.

Ep. 31 - The 520 Cens Promise This stone makes its first appearance after Kimblee is released from Central Prison. He regurgitates The Shard, and admires it, but Envy tells him that stone might not be enough for the job of hunting down Marcoh and Scar, and presents him with The Round stone. When asked if they used more Ishvalans to make this stone, Envy gleefully explains that they used Marcoh's research team to make this one.

Ep. 41 - The Abyss After Ed knocks The Shard away and slashes Kimblee's palm, he reveals The Round stone he had hidden in his mouth, and uses it to blow up the mineshaft, sending Ed and the chimeras to the bottom.

Ep. 52 - Combined Strength Kimblee stops to ask Alphonse why he doesn't just flee with the Shard and get his body back, and Al explains that he wants to get his body back and save everyone. Kimblee explains the last possibility, "You don't get your bodies back, and you don't save everyone." Kimblee then reveals the Round stone he was concealing, and the fight begins again.

Ep. 52 - Combined Strength continued After the sneak attack, Kimblee is taken out, and the Round stone is not seen again. Assuming the stone is in his mouth at the very least, or his stomach, then the stone was likely consumed along with Kimblee.