Adored by the Network: Along with Persona 4, Persona 3 pretty much established the recent MegaTen fandom. Naturally, Atlus has been very quick to fund all sorts of spinoffs, remakes, rereleases, movies…
In fan circles, the officially nameless protagonist has acquired the name "Minato Arisato (有里 湊)," the name given to the character in the manga adaptation. The Gender Flip protagonist in Persona 3 Portable has been lovingly nicknamed "Minako" (an actual Japanese girl's name) by Western fans. She is also known as "Hamuko" (ハム子) by Japanese fans, loosely interpreting the last character of shujinkou (主人公), which means "protagonist," as katakana.
Other nicknames for the Female Protagonist are "MShe" and "FeMC" (presumably pronounced "fem-cee").
Before the male Velvet Room assistant's name was released, fans referred to Theodore as Malelizabeth, Manlizabeth, and Flight Attendant Kanji.
Some people like to call Aigis and possibly other Anti-Shadow Weapons "Toaster".
Flip Flop of God: After a number of "He's just sleeping" theories popped up amongst the fandom in regards to the Protagonist's fate, The Answer unequivocally states that the Protagonist isn't sleeping, he really is dead; only for Persona 4 Arena to state that he is, in fact, sleeping and not actually dead.
God Never Said That: Some fans spread the notions that Evokers were given the shape of guns in order to entice Akihiko (false: the Evokers existed long before Mitsuru even approached him) and that they "shoot Nyx's feathers" (false: the Nyx Avatar didn't even exist when the Kirijo Lab accident happened, and Evokers have always been meant to simulate real guns.)
That said, Evokers do each contain a Plume of Dusk, but rather than shooting it, it helps assist in the summoning. Nyx has also been around for a long time. See more here, here, and here. Note none of this so far has been retconned, as the Kirijo group's study of the Plume of Dusk is the basis for Labrys' story.
Akihiko's sister, Miki, shares her name with Baofu's lover and partner. An interesting fact is that both of them died, albeit in different ways, and their deaths serve as the source of motivation for both men to fight. Heck, another interesting parallel is how each man reacts to their deaths in regards to their Personas: whereas Akihiko embraces Polydeuces/Caesar and wishes to use it to protect others, something he felt that he couldn't do when his sister died, Baofu hates his own to a degree, since Odysseus indirectly caused his lover's death.
No Dub for You: The movie trilogy seems to be heading in this direction, if the initial release of Spring of Birth is any indication.
No Export for You: Persona 3 Portable had been an example of this in Europe until April 2011. Aigis: The First Mission and Persona 3 Social, on the other hand, have only seen Japanese releases.
In both the Japanese and English version, the Male Protagonist shares a voice with Pharos and Ryoji with good reason.
To a lesser extent, Grant George and Mona Marshall both voice members of SEES and Strega. (Shinjiro and Jin; Chidori and Ken, respectively).
Subverted in the Japanese version in regards to Elizabeth and Chidori, as they never speak to one another.
What Could Have Been: Atlus wanted to bring the other games set in the Persona 3 games, but didn't do it since they wanted to bring the earlier Shin Megami Tensei games in English first.
As far as the game's development itself, it seems that, in addition to battles taking place on-screen instead of changing (like a Random Encounter), Persona-users would use tarot cards for summoning, which is more or less what goes on in both the earlier games and in Persona 4. The evokers were made to better evoke the theme of death that the game is built on.
Apparently, the creators had always intended to let the player pick the Protagonist's gender; for the original release, it could not be implemented in time.
Junpei was originally going to be a romance option for the female protagonist in Portable. One can actually hack the game to see a video of him being the one to find her and hold her at the ending of a New Game+ (link here.) There was also the intention of making Yukari the straight up canonLove Interest for the male protagonist, which was phased out when Social Links were put in the game.
In the first episode of the Persona Stalker Club web show, it's revealed that Shinjiro wears winter clothes in the summer because the Suppressants he takes to control his Persona have not been kind to his internal body regulation.
In the second episode, it's revealed that Takeharu wears an eyepatch because the one eye was taken out by Shadows when he led an investigation into Tartarus.
Word of God states the butterflies are Philemon, who is still around in 3, just taking more of an observer role.
Characters who serve as gods in the Trope Pantheon: