So we have these;
On the RPE+TB (Rapidly Promoted Executive + The Betrayed) route, we got a full stand battle between Henry with [Reference] and Right Hand Man with [Time in a Bottle(Bottled Time)]
On the GSPI+CA (Government Supported Private Investigator + Convict Allies) route, during the distraction scene, we got 3 guys doing the torture dance. And their names at the bio are based on Italian foods (Pasta Primavera, Figaro Mulligatawny and Parmezza Lasagne], just like Abbacchio, Narancia and Pannacotta Fugo. Nice.
In the bio, Dan the Man wanted to be called Dan of Steel, Steely Dan's localized name.
On the Cleaned em' Out ending, one of Henry's stolen valuables include THE Stone Mask from the first 2 parts.
There's even the RPS boy Oyanagi, Ken in the background on one scene. He's even named Ken Janpon.
On the bio, at the StD section, one of the PokeMAN guard is named Joseph Jo, though nameless until the entire series got remastered.
Just to second ya, it is CRAZY, even with all the other references.
