Some I don't see mentioned on the TLDW are Clock Tower 3, Rule of Rose, Mitchigan Report From Hell, and Fighting Vipers 2. I'll quickly go over them.
Clock Tower 3 was a PS2 sequel to the SNES point and click horror game. You play a young girl being chased by a killer. It was almost banned and I'm not sure why. I'm guessing it was you were technically a child. It also wasn't very good as a game by all accounts.
Rule of Rose was kind of similar. A child themed horror game. You played a teenager who is put through various trials by a bunch of sadistic kids. It's a collectors item these days, and as such is said to be one of the best horror games on PS2. The clips I saw of the game were really creepy.
Michigan was another horror game that I think was soft banned in places. I managed to get a copy, but the menus are broken so don't expect more than a casual playthrough from the PAL English release. You play a news camera man filming a monster outbreak. What stands out is the sex themes. You get points for not just filming monsters and gore, but upskirt shots and cleavage shots of the news caster. You could also sneak in on her while she's having a shower, but is FMV and you don't see anything. One of the memorable moments had a news caster turn into a monster with a mouth from her vag, which you then kill by dropping a garage door on it.
I might be making the game sound cooler than it is. But yeah, it's a broken, super jank, low budget horror game for nutters only.
Final game is something different from the others I mentioned. Fighting Vipers 2. It was a fighting game for the Dreamcast and Saturn. The idea is you had armour that could break during the fight, leaving you open to damage but also allowing you to do super moves. It was very minor in terms of controversy due to it's obscurity, but according to magazines at the time, people objected to the character Candy/Honey. Since you could see her underwear when you destroyed her armour, and her bio lists her age as 16. That's the age of consent in the UK.
It's very tame compared to the anime games of today with 1000 year old dragon lolis as Candy/Honey basically looks like a woman, or as much as Sega Saturn would allow.
(I'd post media, but KF is being spotty atm for me.)
Another game I was reminded of is White Chamber
I loved that game back in the day. One of the few point and click adventures I actually enjoyed. Great stuff.