For most books, describing a character's clothing is not necessary. Too much description will bore the reader, unless the books is aimed at people who love clothes. However, it is a good idea to know what your character is wearing, and it is unavoidable in a graphic novel or movie. What is unrealistic for a character to wear?
In some medieval fantasy or historical fiction, an author will want the character to wear armor. But this is not always practical. See Common Armory Blunders for weapons that can get through armor, and remember that armor is very heavy, hot, and difficult to move in. Your character might prefer to travel light.
When giving your character armor, try to be realistic. We all know how cool fantasy armor can look, but just because it looks awesome does not mean that it would be awesome to wear. Simpler, but mobile, armor is better.
In certain circles, it is assumed that a woman will wear something along the lines of "sexy" armor: metal or leather that covers certain parts of their bodies. This is only fanservice. It is entirely impractical, especially when it leaves the woman's stomach uncovered. A stomach injury is often fatal, so no warrior would protect part of her body and leave that bare.
When someone is undercover, he or she wants to fit in with the crowd as much as possible as not to stick out. He or she would dress just like the people around. It's best to hide in plain sight. Because of this, ninjas would dress like ordinary farmers -- at least during the day.
If a character were trying to not be seen in a situation where there were not many people around, wearing black would not be the way to go. Shadows are not actually black: they are the darkest possible shade of the colors around them. Inside, very dark brown might be the best color to hide in the shadows with, and outside, "midnight" blue would be preferable. However, if looking normal is possible, that should be done.
Perhaps one of the most annoying aspects of women in movies is their tendency to wear high heels. Can you run in high heels? Keep this in mind, please.