Here’s my process for finding Independent Bookstores for my TomTom Navigator set of Points of Interest:
1) Find the name/address of an independent bookstore.
2) Google it. (All too often, the most recent hit will be a local newspaper story about how the store has closed after twenty-to-forty years in the same location. I suspect that’s because many indie stores are one-person operations and the bright young twenty-to-forty year old who opened the store back in the eighties is retiring and unable to find a buyer.)
3) On the Google search result page, look at the “People who searched for X also searched for Y” results, to get the names/addresses of more stores.
4) Go to the store’s web page to get the actual address and phone number. Look for photos of the store and directions to it.
5) Go to Google Maps, to the “Satellite” view. find the approximate location, then go to “Street View” for the definitive location.
6) Having positively identified the store, read off its latitude and longitude, copy those, plus the name and phone number from the store’s web page, into the database, then move on.
I currently have 190 names/locations and expect to get more as this progresses.
As starting points I am particularly indebted to IndieBound’s Indie Store Finder, the New England Independent Booksellers’ Association’s member bookstores lists, and blogger Heather who, in her 1000 Words Project (among many other interesting things) heroically visited every independent bookstore in the great state of Vermont, took photos, and reviewed them.
Another fertile source of names of independent bookstores has been the perennial article in some local magazine or newspaper listing (e.g.) Bookstores: Best 5 in New England. Oftentimes I’d already have the stores on the list, but the comment threads, where people remark on stores that they think should have been on the list, are gold.
By the way, if anyone can tell me whether The Book Review of Falmouth, Maine, still exists, I’d be grateful. I don’t fancy driving three hours over there to check it out myself (but I will, if that’s what it takes).
JAMES D. MACDONALD 
Do you also take first-person reports? There’s an indie bookstore local to me that probably doesn’t show up in general searches… Pablo’s on Market, Athens, AL.
http://www.athensplus.com/pablos.htm
I absolutely do take input from the comment threads (see me picking up Rodney’s in Cambridge MA in comments on the last post on this subject yesterday….) but, right now, I’m only doing indie bookstores in the six New England states. Someone else may create a set of Points of Interest for the Sunny South, but I doubt it’ll be me.