One of the most enigmatic groups of Koopa Troopers are the Boos. What are boos? Just whose spirits are they? Contrary to popular belief, Boos aren't actually the "living dead" or ghosts. They are very much alive, but just resemble ghosts. Their ghostlike qualities are due to their natural, pallid, biological makeup, causing people to confuse Boos with true ghosts. Even more confusion ensues because their nature entices them to prefer dreary habitats (such as old, dreary houses), and they delight in scaring and haunting. Despite these similarities, Boos are not spirits of the deceased. They are alive, and the simplest proof I can think of is the fact that Boos can be killed by hammers (not to mention they could be easily killed in Super Mario 64).
Now that we've established, at least to some extent, Boo Biology (Boology, hardy har har), let's examine their motives. For what reason would Boos be a part of Bowser's army? They are part of Bowser's troops because those prejudice mushroom people are too afraid to let Boos hang around the Mushroom Kingdom (I can elaborate on that, but elect not to).
One of the greatest Boo mysteries is: Why don't the Boos like being looked at? The reason Boos cover their eyes when Mario looks at them... well, this might not explain it, but when Mario receives his first letter from Princess Toadstool in SMB3, it says something about "Beware of the ghosts. They will give chase if you turn away." And then she says how she has "enclosed a jewel that helps protect you." I always thought that the jewel is what caused the ghosts to cover their eyes.
And there you have it, the Boos have been explained ^_^