Your control over something is controlled by a file's permissions. The system has its controls over some things, you have control over some, and various others have control over various other things of theirs. If permissions are mucked up, a certain program may not run, a helper utility may cause random and unexplained behavior. Usually installer programs mess permissions up, but over time as programs play with these they are not always set back correctly.
Its basic maintenance, to be run whenever you have an urge to do it. I do mine every three months or so, but before every major software update at the least. It doesn't take too long, maybe 20 minutes max.
Also, RAM can help in determining your computer's speed. More on that later.