Is there a a standard source for finding out what businesses (with brick and mortar locations) exist in a geographical area (particularly in the U.S.)? This doesn't necessarily have to be a geographically-based query, but I am looking for city/state/government records or business registration as opposed to something that relies on user-submitted information (e.g. google business directory).
If you're interested specific geographic areas (as opposed to everywhere in the US), you can check with local governments (usually county) for FOIA-able occupational license data and/or data about property records, usually available via tax assessors office, which will often contain ownership information and flags for commercial properties.
A service at Florida International University called TerraFly has tons of geocoded business records. I'm not sure what all their sources are, but it might be worth your while to reach out to the researchers there. I think they have some API access.
[Disclosure: I'm the co-founder of OpenCorporates] Given this site is about 'open data', I'm assuming that the questioner wanted to know about those with a licence that conforms to the Open Knowledge Definition.
There are to the best of our knowledge no such sources of data under an open licence. All the proprietary ones (D&B, Lexis-Nexis, Jigsaw, etc) have restrictive licences, and high price tags. We weren't familiar with TerraFly, and it's not terribly clear what their sources are (white pages?), but would love to know.
OpenCorporates has millions of registered or legal addresses, but these are often unrelated to the physical locations. We're looking at physical locations, but we're not there yet, not least because US business registers don't collect this data, and so we're looking at other public sources (e.g. business licences).
OpenCorporates scrapes the business entity reports for many countries and multiple US states. But its focused on "legal entities", not brick-and-mortar stores. The CorpWatch API has some minimal information on U.S. publicly traded companies and their subsidiaries, but again the locations are legal addresses not physical locations.
Perhaps the best source for per-location business data is the Nets database, which uses the DUNS numbers from Dun and Bradstreet to map "business type, location information, employment, sales, Dun and Bradstreet ratings and payment performance, and special indicators like minority- or women-ownership and whether the establishment imports or exports". They're especially interested in business relocation and claim to "have the latitude-longitude of all origins and destinations of over 4.2 million moves".
As you can imagine, the pricing is obscene -- just $200,000 for the complete 40-odd million records, with the smallest chunk of data going for $2,500. The way it was explained to me is that Dun and Bradstreet collects this info on an ongoing basis, but the most valuable part of it, to them, is what's current, so they sell the out-of-date archive to the folks who put NETS together. There's a 25% discount for "research"...