[quote] For those that watched the show, was this an actual thing in the show? Did they intentionally poke fun at the characters confusion

Absolutely. It happened pretty early on in the show, so I don't think it was catering to the fans.

I think the writers saw the chemistry between Jared and Jensen, and started writing gay one liners. Not about each of them separately, but about them - together.

The first time I noticed it was Season 1 Episode 18 "Something Wicked."

Sam and Dean are checking in to a motel, and a smart-assed little kid is at the front desk.

Dean walks in and asks for a room, while Sam is outside next to the car.

The kid asks, "King or Two Queens?" Dean replies, "Two Queens." Then the kid says, "Yeah, I bet." And makes a funny face.

Then his mom walks in and says she'll take over. He looks at Dean, then looks at his mom and says, "Two Queens." Rofl.

It was hilarious and unexpected, and I think it was the spark that lit the "Wincest" fire.

There's no way it was started by fans, because this was the first season, when the episodes were already written before the show even aired!

Then again in Season 2, Episode 11 called "Playthings."

Sam and Dean are checking into a hotel, and the lady asks, "Are you antiquers?" And they figure they can use it as part of their undercover act, so they say "Yes." Then she says, "I thought so. You look like it. So, one King Size bed?" Lol I think that scene is shown in op's video link.

It really seems that the writers were doing this from the very beginning, and doing it intentionally.

Don't ask me why, but I found it hilarious.