Meanwhile, Hol Horse has a few lines from the Engineer from the same game...
Hol Horse: "Polnareff sappin' my stand!"
Hol Horse: Well don't that just beat all...
Hol Horse: Teleporters, F**k yeah.
Throughout the series, Joseph is a living tribute to Optimus Prime. After Hol Horse escapes near the end of episode 4, Joseph remarks that "they lost a comrade (Avdol) but gained new ones. (They didn't.)" At the very end of the original series, Joseph's ending speech is directly lifted from Optimus' ending speech in the first Michael Bay Transformers movie.
Episode 9 has so many it's hard to keep track, so here's the best way to sum it up: Kakyoin = The Matrix and X-Men, Joseph = Transformers (And it continues in the Series Finale) and about 20 others, and Jotaro has the floating Steve Buscemi head.
Dio: And so, you are left alone... like a rainbow in the dark.
To wit, Kakyoin remarks about how at hospital, he was looked after by a nice lady named Jean...Monochrome or something who hailed from Phoenix, Arizona. When asked if he showed her his one eyed monster, Kakyoin replies that he didn't but she gave him a pair of Summers Edition ruby-quartz sunglasses.
And Joseph's dialogue in the same ep includes Optimus' "One shall stand, one shall fall" proclamation which Dio answers to with Megatron's "I'll kill you with my bare hands!" line (He didn't know the rest but Kakyoin's final Emerald Splash managed to stop him.) Right after that, as Joseph snares Dio in his Hermit Purple, he quotes Optimus' infamous "Booby trap" line from the G1 cartoon.
Episode 8: Let's see, a guy (Kakyoin) saving his friend (Joseph) from a bad guy (Dio) as a certain song plays and a certain sound effect from his weapon (Hierophant Green) charges up...nope, I got nothing. Zip, nada, zilch, Zero.
D'Arby in episode 7 quotes the first few lyrics from Motörhead's Ace of Spades. Joseph even responds to that by humming the first few notes of said song.
D'Arby: If you like to gamble, I tell you, I'm your man. You win some, you lose some, it's all the same to me.
Dio quotes Ozymandias's "I'm not some Republic serial villain" line during his and Jotaro's battle.
"Now that we're in Dio's lair, we should think of a plan to—" "KOMBAT TIME!!!" *smash*
N'Doul in episode 6 is equal parts shoutout to Toots (Being blind and his catchphrase referring to his blindness) and to Ray in his tragic backstory, which Jotaro is quick to point out.
Episode 6 features a number of musical references to Dissidia: Final Fantasy, using "Battle 2 -arrange-" from FINAL FANTASY IV" for Geb's attack on the truck, "Battle 1 -arrange-" from FINAL FANTASY IX" for when Jotaro goes to retrieve Iggy, and "The Order That Must Be Protected" for N'Doul's death scene.
While Jotaro is trying to look for Iggy to help him find N'Doul...
Just before he and Jotaro trade their final blows near the end of Episode 10, Dio quotes a passage from Shakespeare's King Lear.
Jotaro remarks in episode two that a girl has the strength of a tiger...or Beth Phoenix.
In "Doppio was phone?", one of the callers who accidentally dials his number is Roman Bellic. ("HEY COUSIN, YOU WANT TO GO BOWLING?" "Umm...I think you have the wrong number-" "Oh, I got the wrong number, okay okay, das vidanya.") Oh and for kicks, Roman ends up accidentally calling Doppio thrice. On the third time, Doppio EXPLODES at him.