Good question! Answering it is fraught with peril, but I'll wade in anyway.
First of all, I don't think there's a definitive answer because it's a little bit like the Ford/Chevy argument. That being said, there are few differences, at least in terms of raw quality. By that I mean there is little difference in the materials used in the construction of the watch. That is not to say that there are not inferior watches, because there definitely were. For example, the vast majority of NY Standard watches were low grade, and they were meant to be.
But, very generally speaking, the more common manufacturers really produced very similar watches, so you really have to look at the grade of the individual watch because they all made watches of various grades. Quite honestly, a plain old 7j model 83 Waltham doesn't compare with a model 92 Waltham Vanguard any better than a 7j Elgin does. In other words, it really comes down to how well a watch was finished, at least in my mind anyway. And there is something to like about them all!
On the other hand, to me it doesn't get any better than the Waltham American grades.
So, with all of that out of the way, I think a good (VERY GENERAL) list might look something like this:
Waltham, Hamilton, Elgin, Illinois, Rockford, Ball, Aurora, Howard, Hampden, South Bend, Fredonia, Peoria, New York Watch Co (not NY Standard), Lancaster.
I'm sure I left out plenty, and my apology to anyone if I missed your favorite!
The important thing is to look at as many watches as possible, and learn to grade them on finish, condition, originality, and rarity. And by all means, seek out a mentor.