I'm not sure if I qualify as knowledgable, but here goes:
Magazine Enterprises, a division of Sussex Publishing. Probably most famous for their A-1 series, home to the original Ghost Rider, a western hero, and Thun'da, a jungle hero, issue #1 of which series is the only comic ever drawn entirely by Frank Frazetta.
United Features Syndicate, a newspaper-strip-to-comics-format publisher.
David McKay Publications, home to the Phantom, Jungle Jim, Krazy Kat and other comedy & adventure strips.
Harvey Publications, a publisher that was targeted almost as bad as EC by Dr. Wertham for their horror and mystery line of comics.
Lev Gleason, publisher of Boy Comics (later Boy Illustories, starting with issue 43), and many true crime and law enforcement comics, as well as various children's genre titles, such as Adventures in Wonderland.
Superior Comics, a Canadian publishing company.
D.S. Publishing Co. another of the pre-code companies cited by Wertham for their crime and horror titles, and subsequently pushed out of business during the CCA purge.
That's all I can think of right now, off the top of my head, but there are quite a few more that I know of, just can't recall who or what they were or what they published...