I swear I may be the only person who has never actually had a bad experience at Waffle House lol whenever I go it's always just been myself chilling out and drinking coffee with no else there other than the staff, or with one or two friends and it's just as quiet.
I used to be in a shitty local band (well a couple of them) and we would sometimes go to WH at 2 or 3 in the morning. I saw some interesting people for sure. And I have been there many times at all hours of the day. I've never seen anything remotely like the internet horror stories. Obviously there have been fights and shootings and what not at Waffle Houses, but those happen at plenty of other places, too. I think the "shit show rep" that it has just comes from bullshit artists on reddit trying to sound edgy or funny. I saw a lot more weirdness on the handful of times I've ridden a NY subway.