It is daunting to realize how much the subconscious knows without telling us.
One of the most telling examples of this can be found in a fascinating condition known as “blindsight“.
As a result of certain types of brain lesions, people can lose conscious awareness of their vision. That is, they become blind. But, only consciously blind. Their eyes work and their brain still receives visual input. It is only their conscious awareness that has become disconnected from the visual input.
In people who suffer from blindsight, the subconscious can still see perfectly fine. This can be demonstrated by placing an object in front of them and asking them to make a guess about it on instinct. Is it a triangle or a square? Is it red or green? Although they cannot “see” the object, their guesses will be remarkably accurate. Much more so than random guesses from those who truly are blind. Now, if you simply asked them where the object is, they would not be able to tell you. Only if you force them to hazard a wild guess will their answers become accurate!
In many cases, your instinct is also much faster than your conscious awareness. Daniel Smilek, a neuroscience professor at the University of Waterloo, studied the speed that people were able to find a specific object among a bunch of similar objects. Kind of a like a visual search for a needle in a haystack. He found that relaxing and going on gut instinct is much more efficient than consciously searching for the target. Here is a quote from the abstract:
In Experiment 1 participants were instructed to search while either actively directing their attention to the target or by passively allowing the target to just “pop” into their minds. Results showed that passive instructions led to more efficient search on a hard task but not on an easy task.
These findings suggest that the efficiency of some difficult searches can be improved by instructing participants to relax and adopt a passive cognitive strategy
His study is entitled “Relax! Cognitive strategy influences visual search”. Cognitive Daily has an online recreation of this here (and I personally experienced very similar results on this).
Another shining example of subconscious perception is our ability to “pick up” on the mental states of other people. Maureen O’Sullivan, a psychology professor at the University of San Francisco, has spent many years studying people who have the uncanny ability to detect lies. Despite what Hollywood would have us believe, lies are often extremely hard to detect. Many people make more eye contact and fidget LESS while lying. Yet, there are a talented few among us who are incredibly accurate at distinguishing truth from a fib. Much like the blindsight phenomenon, O’Sullivan says that human lie detectors are usually completely unaware of how they do it. Due to extensive social experience, and perhaps some built-in talent, their subconscious is able to interpret a huge range of nonverbal cues to reach an accurate conclusion.
A few years ago, I met someone with a similarly impressive ability to read nonverbal signals, and spent several months working with her. Looking back, it really was an interesting encounter. But at the time it was quite nerve wracking. Similar, I imagine, to hanging around this guy:

(yes, that’s the mind-reading cop from Heroes)
Of course, there is a time and a place for gut instinct. Certain decisions should be carefully considered and weighed. Financial decisions. Career choices. Stock picks. Buying a house. The name of your first born.
The best advice we can derive from research on intuition and the subconscious is this:
Relax! And always make a mental note of your instinct and first guess. Use that as a guide for a conscious decision.