The first known altered photograph was taken in 1847 by Calvert Richard Jones, a welsh photographer who practiced the calotype process. Calotypes were the first photography process which created a negative and allowed for multiple prints – daguerreotypes create a single, unique image. It was altered by painting over the negative with ink to remove a person from the image – on the final photograph, the ink would appear white (when the colors reverse) and be indistinguishable from the sky. We know it was altered because the original, unaltered paper negative survives.
Altering photographs has been extremely common since the beginning of photography. For example, early photographic processes could not generally capture both an image of the ground and the sky – either the ground would be too dark or the sky would be too light. So early photography studios kept pictures of clouds on hand that they could combine with landscapes to insert a cloudy sky into the photograph.
There is an excellent book called Faking It: Manipulated Photography before Photoshop - Google books has some pages available as a preview, which is where I refreshed my memory on the Jones photo. But I highly recommend the whole book if you’re interested in this topic.
What do you mean by doctored? As in the photo was staged, or that the photo was altered after the fact to represent something that did not truly happen?
I do know that most photographs of Civil War battles are staged, as in the photographer would arrange the dead bodies to his liking vs. photographing them were they actually died.
One of these two very famous photos showing the aftermath of the fall of Sevastapol during the Crimean War was staged by the photographer.
I cannot say that it is the first, but it is certainly both a very early staged photo and a very famous one at the same time. Erol Morris, of the NYT, did a blog write up on it about 8 years ago, where he investigated which picture came first, the one with the cannonballs on the road, or the one with them off the road. I'll let you read it yourself to find out what he found.