Stone Free is a string Stand - the third String Stand in the Joestar family, after Joseph's Hermit Purple and his daughter Holly's Stand.
Stone Ocean takes place in Port St. Lucie, Florida. If one was to look closely at its most notable residents, former rapper Vanilla Ice also lives in the east coast Florida city as well. A possible hidden hint of Dio's minion's plans to come?
Jotaro appears as if he never aged a day in Part 6. You know who are also Older Than They Look? His grandfather, Joseph, and his great-grandmother Lisa Lisa, who have the ability to make themselves younger. It comes with two theories: Either somewhere down the line, Jotaro learned to use The Ripple, or Stands have something to do with it.
Alternately, a very Doylist answer would be that Jotaro just isn't drawn older, making his age seem more of an Informed Attribute.
The fight with Marilyn Manson is an Inversion of the D'Arby fights in Part 3, despite having similar abilities. The Stand takes physical life (organs) rather than spiritual life (souls), the bets it collects on are based on real-world monetary value rather than being things that are agreed by bettors to be of equal value, and it has the opposite attitude towards cheating (rather than cheating being an important part of the game, it's the bettor's skills as a Rules Lawyer that are important). Oh, and instead of being beaten by forcing the Stand user to admit defeat in her heart, Jolyne simply beats her into unconsciousness so the Stand will de-manifest.
Each of Dio's sons who appear in this part have abilities similar to his own:
Rikiel's Sky High controls rods, beings that suck the heat out of their surroundings to decrease the temperature, much like Dio's ice abilities sucking out his opponent's heat to freeze them in their place.
Donatello's Under World traps his opponents in past events they cannot escape, often tragedies that resulted in many deaths. Dio's time stop also traps his opponents in an unescapeable scenario, and the ability to revive past victims could be a call-back to Dio's ability to create zombies.
Ungalo's Bohemian Rhapsody drags people into fictional stories, with most characters coming out as twisted, parodic versions of their original selves. Other than the example mentioned above, it's also a call-back to Dio's ability to create twisted living beings from fusing animals and humans.
As Pat and Woolie pointed out, Jolyne's final move in part 6 (using her string to attach Emporio on a dolphin, banking on the fact that Pucci, due to Made In Heaven's time-accelerating powers, also has accelerated breathing and thus cannot chase Emporio underwater) looks massively out of place considering the endings of the other parts. But it's actually a massive Call-Back all the way to part 2: Joseph Joestar's ultimate technique running away. Which is what he did against Kars.
Giorno's lack of involvement in this part makes some sense outside of Superman Stays Out of Gotham. The two sides that are fighting are his father's closest friend, yet is the Big Bad, and the man who murdered his father, who just happens to be the Big Good. In a way, it'd be like how Fugo left Giorno's group.
Compact discs seem like a strange way to contain Stands until you consider that most Stands are musical references.
Star Platinum is a Tarot themed stand, and probably wouldn't normally fit...unless if you consider the idea that they're Tarot Cards. What is another type of card that stores things? Memory cards. And what is an upgraded form of a memory card? A compact disc.
Once the powers of Made In Heaven are activated, everyone seems doomed... up until Rohan Kishibe is mentioned to be still meeting his deadlines. How? He could have easily just written "thinks at an accelerated pace" onto himself using Heaven's Door to continue writing his manga.
He could have also wrote "Unaffected by this attack" or booted himself into a different universe as Pucci activated Made In Heaven.
In Stone Ocean, when Pucci accelerates time, he's able to move normally compared to everybody else. That means Pucci waited for trillions of years after killing Jolyne just so Dio could achieve his dream.
During Made in Heaven, we see that Rohan Kishibe from Part 4 was able to keep up with his manga deadlines even as the world accelerated and everything around him died, possibly suggesting that he had gone into the next world unscathed. This means everything he's familiar with has been replaced with alien people and places he knows nothing of. But hey, at least Josuke's not around anymore!
And just to add insult to injury? Josuke would still be alive because Made In Heaven only reincarnates people who died..... meaning yep. Josuke still gets to annoy him.
Speaking of Part 4 and Made in Heaven, the fact that the lovable band of buddies and unusually low body count of Diamond is Unbreakable are all for nothing. What was in store for Josuke, Koichi, Okuyasu, Tonio, Yukako, Hayato, Yuya, Mikitaka... The list goes on, but point is, what's in store for them all? The horror of Made in Heaven advancing time as they can do nothing to prevent it. At least the Part 5 cast were vicious mobsters.
If what happened to Emporio is any indication, it's entirely possible that they survived in some form after all, the only characters other than Emporio we get to see in the alternate universe are ones that died in part 6; it's entirely possible that if you survive Made In Heaven's time acceleration, you get to go to the new universe unharmed and unchanged, whereas if you died during the acceleration, you get turned into an alternate version of yourself.
The question is, if theyre unchanged, how are they gonna react to Nu-Jotaro and Irene?
We know that Polnareff was still around inside of Coco Jumbo at the end of Part 5, and if Purple Haze Feedback is any indication, is second-in-command at Passione to Giorno. However, while Coco Jumbo was still a living being, Polnareff was merely an soul who had yet to ascend that was living inside of a Stand. Considering that Made in Heaven's time acceleration has the ability to take adrift souls and place them into new bodies, which also applies to the universe after Pucci is killed, does this mean that Polnareff is no longer Jean-Pierre Polnareff, suffering a similar fate to Nu-Jotaro, Irene, and Annakiss? ...Joseph must be weeping of loneliness.