I've heard from various online videos or articles of pros talking about how National Geographic doesn't allow this or AP doesn't allow that. Does anyone know if these rules are written down somewhere or are can we generate a list of guidelines for what is/isn't allowed?
Most news organizations have their full guidelines listed in areas accessible to their contributing photographers. Some organizations publish part or all of their policies openly as well. Even within the same organization, the rules may be different for different types of editorial content such as sports, hard news, features, etc.
A good place to start might be one of the standard texts used to teach college level photojournalism courses. Kenneth Kobre's Photojournalism: The Professional's Approach is currently sold in an updated 6th edition. It includes chapters on Editing, Ethics, and Law, as well as the History of photojournalism. Individual chapters on various types of editorial content such as Spot News, General News, Features, Portraits, Sports, Photo Story, Video, and Illustration also discuss what is generally accepted within each category.
Many examples are given along the way. Well known cases, such as Reuters contributer Adnan Hajj's manipulation of the smoke over Beruit after a bombing attack, are discussed. So are less publicized cases where, for example, a photographer lost his job after he was observed moving a Coke bottle out of a scene before taking a spot news shot.
To show that AP mean what they say - they have recently applied a rule in their list which is cited by AJ Henderson above viz
'No element should be digitally added to or subtracted from any photograph. The faces or identities of individuals must not be obscured by Photoshop or any other editing tool. Only retouching or the use of the cloning tool to eliminate dust on camera sensors and scratches on scanned negatives or scanned prints are acceptable ...
Minor adjustments in Photoshop are acceptable. These include cropping, dodging and burning, conversion into grayscale, and normal toning and color adjustments that should be limited to those minimally necessary for clear and accurate reproduction...'
and "cut their links with" Pulitzer Prize winning freelance photographer Narciso Contreras after he edited a photo to remove a video camera visible in the cornner of a war scene photo.
The page is worth looking at as much for the extensive for & against reader comments - which give an idea re what photographers in general think the rules are, or should be.