It depends on what you want to detect. If you want to detect any manipulation at all, then there are some techniques that you can use somewhat effectively. If you want to detect fakes like with bigfoot and Nessie photos, then the options are more limited. While there are actually more signs of a doctored photo, the problem is that they tend to give a lot of false-positives.
When an image is doctored or manipulated, is there metadata embedded in the altered image so that one can know it is a manipulated image?
It's possible, but if someone were going to fake a photo (at least with enough skill for it not be an obvious fake), I would think they would be smart enough to disable or strip any metadata. Even so, the metadata would only indicate that the image had been saved by some program or another, not what was done. For example, someone may open a photo in a program, then save it as another format, compress/optimize it, or resize it. If the program adds metadata to the file, it does not indicate "doctoring", or even necessarily manipulation, only that the program created it (the file, not necessarily the image).
Or is there some other tool or method that can assist?
There are a small handful of programs/plugins that can perform some level of analysis on a photo to look for abnormal artifacts like incorrect edges (as when an item is artificially inserted into a photo), or improper blending, etc. The problem is that most of these can be caused by standard manipulations and so are not reliable ways to detect actual forgeries.
Can I use Photoshop to detect or find out with 100% certainty if an image is altered or not?
You can use Photoshop to manually search for most of the artifacts that the programs/plugins look for. For example, try zooming in to see if you can find image artifacts from the image being re-saved/converted/etc., but that could very well lead to false positives since a non-docotred image would exhibit similar artifacts when saved, compressed, etc.
I was reading some news about fake UFO photos and this question came to my mind.
When it comes to things like this the best and most effective tool is ultimately your own mind. Use common-sense to detect some fakes like photos of Obama eating an alien while riding a unicorn. For more realistic fakes, use your mind to detect things like incorrect shadows or "Photoshop fails":