Johnny,
There are some clues a savvy person can use to determine if a digital photo has been manipulated or not. Typically a photo coming straight off a camera contains EXIF data which tells all the settings used by the camera when the photo was taken, f stops, light levels, shutter speed and even the make of the camera. Heavily manipulated photos do not contain this data, it is possible to fake the data but the average armchair railroad photographer is not going to go through the hassle of doing such a thing.
The thing about photomanipulation is simply that its nothing new. I've seen countless photographs published in books that have been altered by either historians or even the photographer to spice something up, a quick example off the top of my head would be an early shot in the Pacific Coast Railway book by Gerald Best, if one looks at the tender you can tell that the image was played with. I've seen a handful of NCNG photos that have been manipulated by the photographer to make something appear as something else. To make matters worse, doing research on a photo does not always provide a clear answer, I have in my personal photo collection several photos with notations by the photographer that are simply not correct. I've even had the joy of going through photos in museum collections with docents and curators to provide input on when and where a photo was taken, trust me you've never been frustrated until you know what something obviously is, but the person cataloging the image "wants" it to be something else and argues with you making notes
their way.
The ultimate truth is, this whole mess has been going on for over a hundred years and its not going to change or probably get worse.
-=Andrew=-