Oh, the FEELs that I have about this one!!! (And kadollan and I might actually be writing an HP fusion story so we may have talked extensively about this very point.

So.

Natasha - Slytherin, no question.
Clint - also Slytherin. He's a survivor, and he's sneaky.
Tony - "I have a plan. Attack!" (Does this ring a bell? The Gryffindor motto should really be "Everyone on three!") Total Gryff.
Bruce - Ravenclaw (again, this didn't take any real thought on our parts.)
Pepper - she's never had a problem doing what needs to be done, and while she'd probably make a damn good Slytherin, she's absolutely a Gryffindor.
Jane and Betty are both Ravenclaws, hands down. (Yeah, the scientist thing is kind of a gimme, and I could make a case for Betty being a Gryff, but in the end, I think Ravenclaw is the best fit.)
Darcy (well, ok, my headcanon Darcy) is totally a Slytherin.
Loki would also be a Slytherin.

Now we get to the tricky part of all of this, Steve and Thor.

And I lobby really, really hard to put both of them in Hufflepuff. Thor, because what we see time and again from him is loyalty - particularly to Loki, but also to the friends he makes along the way. Yes, he's strong and brave, but the loyalty thing... that's what I've gotta go with.

And for Steve, again, there's a loyalty aspect, and also a talent aspect. Between the two, I'd have to put him in hufflepuff. Which also kind of fits with his "starting out as an underdog" storyline.

We've done Peggy and Bucky, too - I think Bucky ended up a Gryff and Peggy a 'Puff, but I could have that backwards? Or mistaken, it's been a minute.