I was thinking about the topic of emotions, and their reliability in different areas of study(science, history, math etc.). The question I have is: Can we know when our emotions are credible in the pursuit of knowledge? For example, pseudoscience is caused when emotions trump rational thinking; so, is there ever a time when we can be sure our emotions are not deceiving us in the pursuit of knowledge?
You have misidentified the cause of pseudoscience, it is not emotional thinking, people generally believe things based on their direct perception, the emotions come later.
The pseudoscience is usually due to the genuine altered perception of people, altered by individual differences in wiring or by hypnosis, meditation, brain damage, psychoactive drugs, as well as training in perception by studying the arts. The persistent recurring topics of pseudscience almost always have a basis in a definite perceptual phenomenon, that you should try to experience, try to isolate and study in people, because it isn't bunk:
ESP: this is synchronicity plus the back-dating perception, where someone will tell you something, and you feel that you already knew what they said before they said it. There is also the effect of nonverbal cueing, and various social signals that are barely perceptible. The synchronicity of thoughts is real and easy to demonstrate statistically, especially among people who know each other well or who share a common literature background, and so can predict each other's thoughts. These phenomena are not supernatural, but the perception of ESP is stronger in people who are sensitive to these things, and they want science to validate their perception, not their emotion. It's not going to do that more than I just did above.
Auras/Orgone energy: The "energy field" of people is something people actually percieve, as a vague glow surrounding a person, something like an after-image, in a color that James Joyce called "heliotrope". It's there to percieve, you can see it, it's just not made of matter and the only instrument that can detect this afterglow is the human brain. It is perceived relatively stably by people trained in visual arts, or who are socially sensitive, or who are high, and these people see something there, so they want a machine that will detect this. That's hopeless, because it is purely perceptual, but that doesn't stop people from making orgone machines. The halos of religious iconography are representations of this.
Conspiracy theories: This is the perception of collective agency in the world--- an intelligence due to a collective making a decision that is not due to any one person, and fallaciously concluding that since all intentional action must be due to individual people, or to groups of people in collusion, that the collective coherent effects are due to a conspiracy in a small room. There are a handful of actual small-room conspiracies, but most of the truly vast conspiracy theories emerge from misattributing the thoughts of the gods to one person or to groups of people actively holding these thoughts. There was no "DMV conspiracy" to make the experience at the DMV miserable, likewise there is no "beaurocrat's conspiracy" to make paperwork onerous, although you wouldn't know it based on the results.
UFO/hollow-earth: This is due to actual hallucinations people have, drugs speed this along, and also some rare physical phenomena like ball lightning. The idea that there are other intelligent agents in the world other than people is completely reasonable to a lot of people, considering the collective agency of the gods, and people see gods everywhere, and those who don't call them gods end up calling them something else.
Other things called pseudoscience, like perpetual motion with magnets, are just bad or discredited science, not pseudoscience. This includes most pseudoscience topics. Other pseudoscience, like radiation hormesis or cold fusion is just open questions, and there pseudoscience is used as a poltical label to clobber people working on something unpopular.
The emotions that come with ideas are usually posterior, in that one makes up one's mind early, and later, one has an emotional reaction to something that disagrees with what you believe because you already decided you didn't like it a long time ago. This is just personal mental shorthand, and it has no real significance as far as I can see. Emotions don't get in the way of evaluating propositions, it doesn't matter if you're hotheaded or cool, or how much you like an idea, just so long as you reason it out regardless of how you feel about it. For example, twenty years ago, I hated, hated, hated S-matrix theory, because I thought it was preposterous and I couldn't see how it could work, but as I learned more about it, I finally couldn't see anything wrong with it, and now I think it's the super-duperest coolest thing evar! So what. It's still right regardless of how one feels about it.