So, as the title explains the post, I'll just start with the list.
1) The letters spelling out JOJO at the very start (The ones with all the protagonists inside) is a direct reference to the B cover of Chapter 321.
2) The word BREAKDOWN exploding and reforming is a reference to Joskue's anime theme, and the abilities of Killer Queen and either Crazy Diamond, or Bites the Dust's time loop.
3) Behind the first BREAKDOWN is an image of Killer Queen with mechanical arms, most likely referencing the technical aspect of bombs, or KQ's primary bomb, while the way it is posed is a reference to the pose it strikes in Chapter 326.
4) The afterimages left behind by the protagonists reference both their lasting influence on Morioh, and their many iterations due to the effects of Bites the Dust.
5) The looping effect that occurs in Rohan's house may be a reference to his 'Bizarre Adventure' in Reimi's alley, or his death loop caused by Bites the Dust.
6) If you look closely at Rohan's shadow during the first looping sequence (Where he is drinking from a mug), you can see Cheap Trick on his back.
7) One of the crop circles that can bee seen in the same shot as Super Fly is the one Mititaka was found in.
8) As Shinobu's afterimages continue on, she gets more and more depressed, referencing her loveless marriage, and her attitude in general.
9) The scene that is referencing the painting 'Golconda' also represents the several candid shots of workers that Rohan took.
10) Rohan's pose after the first shot of Reimi's hand pointing upwards is a reference to page 12 of Kishibe Rohan goes to Gucci.
11) During the transition of Rohan and Yukako posing to Jotaro, Koichi, and Okuyasu posing, the motorcycles that Hazamada knocked over during the Surface arc are visible.
12) The golden light behind Reimi's hand in the second scene where it is visible may be a reference to the 'Golden Hearts' of the protagonists, as mentioned in 'Goodbye Morioh Town, the Golden Heart'.
13) The perspective of the shot where the protagonists are pointing to the sky is similar to that of the cover of Volume 39.
14) The first 9 in the '1999' near the end of the opening bears reference to Terunoskue Miyamoto, and his Stand, Enigma. The puzzle pieces bear reference to enigmas in general, and several items that Terunosuke keeps folded in paper are visible, such as the Handgun, the Acid, and the Scorpions. In addition, Terunosuke is visible on the far right hand side, holding a folded piece of paper.
15) The second 9 in the '1999' is a reference to Ken Oyanagi and his stand, Boy II Man. The black design around the hole references his clothing, while the center is the hole in his cheek. The hand that pops out of the black circle in the center is a Rock from Janken, while the bottom of the 9 represents the Scissors.
16) The scene with Kosaku-Kira and the word KILLA on the ground is a reference to the cover of one of the later chapters. (I forgot which one, but all I know is that it's chapter 2 of an arc. If anyone knows the chapter's name, please do write it in the comments.)
17) Around the JUSTICE clock in the end card are several vines from Hermit Purple.
And that about does it! If you have anything to add, please do leave a comment. <3