I am in no way trying to say that human beings should be emotionless, nor do I think that emotions are the only thing that drive your thoughts other than your consciousness. I do, however, think that emotions impede rational thought.

For example, an outburst of anger towards a relatively innocuous event, which is common, can hardly be described as a conscious thought. It is certainly a thought, but not one you make consciously, it is one you make compulsively. Reactions following this outburst are generally also somewhat compulsive.

There are, of course, plenty of other factors which drive what we think about. As you've already mentioned, biological impulses certainly drive our thoughts. For instance, lets say your stomach is rumbling from hunger. It is safe to say that at this point your thoughts will also be lingering on the idea of getting something to eat. Again, it is tough to say whether these are thoughts that are controlled or compulsive.

The desire for sexual gratification is also fairly compulsive. Though yes, sexual urges can be controlled, I find that thoughts often dwell on this subject when it would be beneficial that they did not, and I would rather they did not.

In adolescents, it is a well known fact that harmones play a role in their behavior. They are more irascible and more susceptible to a wide range of emotions than normal. Again, in my definition, this is not controlled.

Hallucination, though an extreme form of lack of control of thought, is certainly a good example here. Hallucinations can seize control of your thoughts altogether, and more or less anyone is susceptible to them!

Point is, at any given time, their is more than just your consciousness that is governing your thoughts.