I love the original Hotline Miami but I’m not a big fan of the boss fights like the ones in Neighbors (Biker) and Deadline (Van Driver). I find it kind of slows down the game and limits the strategies you can take.
Another example would be Fallout 3. I find the tutorial section in Vault 101 can feel a bit long after a fifth run but maybe that’s because I was spoiled by Fallout New Vegas’ ability to run off in your own direction immediately after leaving Doc Mitchell’s house.
Everyone already mentioned Dark Souls and stuff like that. Some stages in classic Doom are also kinda like that.
But my personal nemesis is the mission Glatisant in Ace Combat Zero. Every AC game has it’s long score attack missions, but Glatisant is mandatory in every run of a game you have to clear at least 3 times, and it’s a 30 minute long ground assault on a snowy mountain range with poor visibility and covered in air defenses. The danger level never gets lower, and it’s easy to get shot down right at the end and having to start it all over again.