About $1,500-5,000 a shot. Depending one what kinda usage your after. And with a real photographer you can get a series of shots that actually work together... with royalty free thats not so easy. I'd much rather hire a real photographer... but budgets rarely allow for it.
Ahh,.. slight correction. A stock photographer IS a real photographer, and does not always submit their images to royalty free stock libraries. In fact, most don't. Some stock photographers get paid in the range that you mention for stock images, more often it's much lower though. Royalty free libraries are a way to get exposure. They're a marketting tool, which is also why you rarely find a photographer's best images in them.
The main difference between stock photography and "real" photography as you call it, is the way that the images come about, and how they are licensed.
Stock images are made by real photographers, they are considered "generic" enough or to have enough mass appeal that they can potentially be used for more than one type of ad or otherwise. Their copyright generally stays with them, but may be sold in part or in whole depending on the scope or use of the image (depending on the contractual agreement)
The other sort of photographer that you're talking about takes "assignments". In general, this is a project for one person or entity, and the copyright remains often with the client, but depends solely on the contract in place.