Most–though oddly enough not all–guidelines mention money at some point. That is, they tell you what, if any, payment you can expect if your story is accepted for publication. There are many variations on this theme.
Many markets pay by the word; in fact, that is so common that the per-word rate is the only indicator I know to distinguish between pro, semi-pro, and token payment/markets, with pro being a rate of $0,05 or more, semi-pro between $0,01 and $0,05, and token below $0,01. There are also markets that don’t pay a penny, but let’s not talk about that yet, shall we?
Then there are the markets that pay a flat rate, usually by length category. For instance, a market might pay $10 for flash (< 1000 words), $25 for short stories (1000-7500), and $40 for novelettes (<17.500). Notice how the rates are fairly low? Convert to per-word rate and you’ll find that these are usually token markets, who apparently don’t want the hassle of calculating the weird amounts that come with per-word rates.
Usually, that’s it. You part with the first publication rights to your story, they part with their money. In some cases, the payment is actually an advance on royalties (mostly when the market is an anthology), but with the sales figures, the publisher overhead, and dividing the remaining royalties among the contributing authors to the market, you will never ever ever earn back your advance, so the royalty bit is purely academical.
A final aspect is when and how you get your cash. The guidelines often mention that, and the contract always should. Most common time of payment is upon publication, which means that there can be months between acceptance and getting your money. Some markets pay upon acceptance, which means that you can spend your money well before you ever see your story in print. Some markets will offer you a choice between check and Paypal. For small amounts, take Paypal. I got paid a token amount for Deep Red (twice), and discovered upon receiving my $10 checks that the cost of cashing them here was higher than their value. So I framed them instead.
