Asimov's, Analog and the Magazine of Fantasy and Science Fiction.
They are pro paying markets that have been around forever. Sadly, of them only Asimov's takes E-subs and that only recently. Kind of funny since Analog is also a magazine of science fact, and yet they are so far behind the times.
They are really the "big three" of science fiction though...Asimov's and Analog only take sci fi, no fantasy horror etc...on the Magazine of Fantasy and Science Fiction does.
Edit: As for how to choose where to submit, thats mostly a personal thing and depends a lot on your particular goals. I recomend Duotrope's Digest for searching markets. I don't have a lot of time now but I'd be glad to share my knowledge of terminology and what I've learned about different markets...feel free to email me should you so desire.
[This message has been edited by Merlion-Emrys (edited July 30, 2010).]
When I think of publishers I think of the "Big Six": Hachette, HarperCollins, MacMillan, Penguin, Random House, and Simon and Schuster. Each of the Big Six are the parent companies of other publishers. MacMillan owns Tor, Random owns Crown, etc.
Maybe you're thinking of "The Big Three," as in Asimov, Clark, and Heinlein?
"The Big Three" in most SF conversations these days, are as follows:
ANALOG SCIENCE FICTION & FACT editor: Stanley Schmidt publisher: Dell Magazines
ASIMOV'S SCIENCE FICTION editor: Sheila Williams publisher: Dell magazines
FANTASY & SCIENCE FICTION editor: Gordon Van Gelder publisher: editor owned and operated
Of course, these are not the only short SF markets that pay pro rate. They're just the ones which have been around the longest, still get the most Name pro writers in them, and earn a lot of awards and award nominations for both editing and fiction.
For anyone who thinks Asimov's only takes science fiction, I'd suggest you read Kij Johnson's "26 Monkeys, Also The Abyss" (it's available online there). World Fantasy Award winner, nominated for both Hugo and Nebula, and won the Asimov reader's award for good measure.
Whatever that story is, it's not science fiction. I'm not saying the Asimov's will take sword and sorcery, or vampire erotica, but their definition of SF is clearly on the broad side.
When I started there were five...and Asimov's had yet to start. Three of those are gone completely. Apparently the SF market can only handle three "Big Three" magazines at a time.
Not that they're very big---look at their subscription base numbers. Not that they pay very much---compare their rates to what non-SF magazines pay, fiction or non-fiction. Not that they're that professional---again, compare them to other magazines, or, better yet, compare them to SF magazines published back thirty or forty years ago.
Well, "borderline fantasy" doesn't tell one much. They say no "sword and sorcery" and from what I know of them I'm pretty sure they wouldn't take urban fantasy in the "Dresden files" vein with direct magic use and all that. They are listed on Duotrope as a science fiction market. What they call "borderline fantasy" is probably something along the lines of "slipstream." They definitely aren't a hard sci fi market, but I can't imagine them even considering straightforward stories where magic or the supernatural are key elements. I could be wrong though.
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Non-fiction article word rate has always paid more than fiction short story word rate. I don't know why anyone is having such a problem with that. Anyone who is overly upset at how much fiction markets pay, would do better to submit non-fiction to the non-fiction markets.
I won't speak for Asimovs or SF&F, but it's been my experience that Dr. Schmidt and Co. of ANALOG are the epitomy of professional. Selling to them has been a very pleasant experience. Stan gets first look at all my stuff now, and whether he buys it or not, he always provides specific critique. I've proven to him that I am a commodity worth developing. The budding relationship is one of cooperation.
Again, if you can swallow some pride and knock a chip or two off your shoulders, you can do well with a market. All it takes is using SMF and comporting yourself professionally, plus turning in a half decent story, and the editors will begin to pay attention to you as someone worthwhile.