Oh, I was going to keep posting in here but I forgot.
How about a megapost? I'll split them up into sections, and I don't think any of them have been mentioned in the thread yet:
Did you know...
Wan Chai/Aberdeen
... that if you learn the Iron Palm (and do the corresponding tree bullying) before you carry crates for the first time, the game will automatically advance time to 7pm?
... that when Xiuying invites you to stay with her, if you stay out until 11pm you'll be taken there automatically? This wouldn't be noteworthy, except that it's accompanied with the line, "Took you long enough."
... that when changing discs on the Dreamcast version of Shenmue II, you can view extra artwork by pressing the triggers?
... that when asking about the mysterious paper found in the Wulinshu, the Da Yuan Apartments are locked until 8pm? This is presumably to force the cutscene where you see Xiuying crying, but there were better ways to go about it. As a related "Did you know?", after the cutscene where Guixiang teaches you about Chawan signs, the game will automatically advance time to 7pm, but only if you haven't yet seen the aforementioned Xiuying cutscene.
... that when doing Chawan signs, there are multiple places with interesting effects? At Blue Sky Garden you'll get a cutscene with Fangmei and Eileen; at Ling Ling Porridge or Canton Cafe you'll get a QTE with the Poison Brothers; at Bai Jiu Stand you'll get a CQTE with what are later revealed to be Yellow Heads; and at Man Mo Bistro you'll get a bit of a runaround leading to a QTE and/or fight.
... that when chasing Ren, you can stay up until 4am? You can also chase the other three for additional fights and scenes.
... that on your last day in Wan Chai/Aberdeen, you can say goodbye to Delin, Eileen, Zhoushan, Zongquan, Izumi, Jianmin, Guixiang, Zhangyu, Jiangyu, and Fangmei, each with special dialogue?
Fangmei
... that if you don't get any information on Yuanda Zhu on your first day of work, you'll get a unique cutscene with Fangmei?
... that talking to Fangmei repeatedly (specifically when she starts the conversation when you go near her) increases her affection for you?
... that after talking to Eileen, both Fangmei's and Eileen's daily routines change? They spend the early afternoon in Man Mo Bistro together; afterwards, Fangmei will spend the rest of her afternoon staring into Complete Clothier's window while Eileen goes shopping in Wise Men's Qr.
... that after raising Fangmei's affection enough, if you talk to Eileen when she is shopping in the Wise Men's Qr. she'll tell you when Fangmei's birthday is?
... that after raising Fangmei's affection enough, if you approach her while she's staring into the window you'll get a cutscene with her? You can go inside and buy a present for her for $150 - you can give it to her by going to the Da Yuan Apartments on her birthday, earning you another cutscene.
... that doing the Chawan sign in Man Mo Bistro gives you a bit of a runaround leading to a QTE and/or fight? Losing both the QTE and the fight gives you another unique cutscene with Fangmei; it also increases her affection for you (but not to the maximum amount as some sources claim).
... that after this event (or after doing the Chawan sign in Dou Jiang Diner) going to Man Mo Bistro in the afternoon gives you yet another unique QTE featuring Fangmei?
... that doing the Chawan sign in Blue Sky Garden gives you a cutscene with Fangmei and Eileen?
... that if you say goodbye to Fangmei on your last day and you gave her a birthday present, you'll get a very special cutscene? You'll also get another one on leaving Hong Kong for Guilin.
Kowloon/Guilin
... that if you fail the first CQTE when handcuffed with Ren, you'll get extra scenes showing them locked up together?
... that when Ren offers you a choice between Heads and Tails, you can press B (or just wait) to choose neither and let Ren make the choice for you?
... that instead of walking across eight planks when climbing the Ghost Hall Bldg., you can enter via Thousand White Bldg. and use six, or via God of Wealth Bldg. and use just five? Alternatively, you can use the map glitch on the stairs and skip all of them.
... that there are nine different cutscenes where the Scout asks to meet you? Depending on which fight you last did, the location and camera angles are different. This is true for the six street fights as well as the Rod, Greg, and Chunyan fights.
... that when the Scout asks to meet you on Dragon St., you can stay up until 2am? The game will force you there afterwards.
... that when the Scout asks to meet you underneath Thousand White Bldg., if you're not there by 2pm the game will force you there?
... that if you arrive early when meeting the Scout underneath Thousand White Bldg., you don't have to wait? You can simply run ahead, and get a different cutscene when approaching the gate. Opening the Dou Niu door will trigger a retry, but the normal cutscene will play instead of this alternate one.
... that when searching for the watchman's room on Yellow Head Bldg. 17F it's possible to check every room in one cycle?
... that when you leave for Guilin, Joy takes some of your money to pay off your Come Over Guest House bill? If you owe Ren Dan more money than you have, she'll take all your money.
... that if you take too long at almost any point in Guilin, the game will simply force you into the next scene? The only exceptions are the QTE sequences, when you're lost and have to lead the way, during Rocky Area, and in the Stone Pit.
Glitches
... that it's possible to clip out of bounds using the staircase in Dobuita? By walking up it at a certain position and running when you're a few steps up, you can turn around and run on thin air. From here, position yourself over the tray outside Komine Bakery and talk to Komine; you'll drop down through the tray. Repeatedly tap left and right and eventually you'll walk through the wall and go out of bounds.
... that if you talk to the people in Nagai Industries while looking for Wong to translate the letter, Ryo will ask them about a china shop - despite the fact that you're not supposed to know about the china shop yet?
... that by doing the stair clip, you can skip almost all of the first disc of Shenmue I? Clip out of bounds and run around the outside of Dobuita, and you can catch the bus before you've even talked to Nozomi.
... that when you're shopping for a ticket to Hong Kong, if you clip out of bounds and go to New Yokosuka Harbor, Shozo has unique dialog, and Ryo will ask everyone else about the Old Warehouse District?
... that if you use the map glitch to skip getting your bag stolen and head to Wan Chai, strange things happen? People give the wrong directions to Wan Chai (mainly because you're already in Wan Chai); Ren Dan's dialog is seriously messed up; the students of the Guang Martial Arts School do starjumps instead of karate; and Jianmin seems to already know you, letting you spar with him while also still holding your bag.
... that if you map glitch through the trigger in Rooftop Fight leading to Worker's Pier, you can see a sign labelled "Worker's Wharf", an early name for the area?
... that if you map glitch through the trigger in Worker's Pier leading to Rooftop Fight, you can enter a second trigger area placed behind the first that just outright crashes the game?
... that on the Xbox and re-release versions of Shenmue II, if you talk to Fangmei, soft reset the game, and start a new game and talk to Fangmei, her affection level and previous conversations won't be reset?
... that on the Xbox and re-release versions of Shenmue II, if you use an elevator, soft reset the game, and start a new game and go to that elevator again, it will be on the floor you last left it on?
... that when following Yuan, on exiting the Tea Break Bldg. instead of heading left and following Yuan, you can run straight to the Moon Child Bldg. and skip everything in between? You can also go through the Black Heaven Bldg. to skip even more!
And finally:
Did you know that you can despawn NPCs in another way in Shenmue II? Use the map glitch to get out of carrying the books, and enter and exit Man Mo Temple to open the gate. Some NPCs will be despawned when doing this, and others won't turn to face you when you talk to them. Still others will walk in a straight line, often directly into and along walls. As a bonus, head to Warehouse No. 10 when the game's in this state. It seems to be some sort of nuclear bunker, because when Ryo leaves again every human and animal on the planet has been wiped out...
... except for one. I call him "God", but others may know him Chengyou Wen, or the baseball darts guy. For some reason he's still there, playing darts.
If the end of humanity is too bleak for you, you can bring them all back by playing Space Harrier or OutRun on the Dreamcast or Xbox versions, or by saving and reloading in all versions.
I think that should make up for the days I've missed.