www.hometownlocator.com is a good one. You can get there a list of every town that has at least a person left, & some that don't. Under historical features they have things like ghost towns with nothing left, post offices, churches & schools that are no longer there, cemeteries. Natural features, current road & satellite maps with parks & schools can also be found there.
Genealogical sites can be good, but it seems there's too much to go through. A large one that's popular is Cyndis List.
Put into a search engine the name of a county you want to research followed by historical society. They almost always know at least most of the ghosts. Sometimes there is a link on the main county govt site to the Historical Society.
Type in the state you want followed by League of Cities. There should be a link to every incorporated place still existing. Places with under about 100 people don't normally incorporate these days, so most of those are probably towns that were much larger. Compare the tiny towns on the League of Cities site (2010 populations) & tiny towns & x-towns on hometownlocater to the 1895 online atlas.
Most old atlases listing populations for un-incorporated towns show populations that are double or triple what they really had. These figures may have been furnished by townsite promotors. For incorporated towns, the populations shown are the exact or preliminary US Census figures.
Wikipedia is also becoming a great site for ghost towns. But they only count totally abandoned places as ghosts. They also have short write-ups of most towns with at least a few people, both places that were larger & towns that never were much. Best wishes, George (MN)
