Word similar to 'insidious' or 'pernicious', with a non-negative connotation

I'm looking to describe an effect caused by using a particular construction in English, and the fact that it affects the listener and the whole of their thought processes without the listener being aware of it. The words insidious or pernicious would almost do, but these have negative connotations. The effect here is neither positive or negative.

The use of (x) has a(n) _____ effect on our mental processes.

That sentence requires an adjective, but an adverb would do just as well :

The use of (x) affects our mental processes _____ .

So, a quick recap. Ideally the word would:

• convey that the process is silent and unnoticed by the speaker
• convey that it spreads through and affects all of the speaker's thought processes
• not have any particularly negative or positive connotation

Solution 1:

A stimulus that is below the threshold of conscious perception, but nevertheless influences one’s mental processes is said to be subliminal, or to influence them subliminally. As the OP requested, characterising some influence on a person as subliminal, does not imply anything as to whether the influence, or the motivation for it, is good, bad, or neutral. The Wikipedia article on the topic provides a serviceable explanation of the concept. The term started out as a technical term of psychology, but quite a few people have by now heard at least some popular outline of this phenomenon to be able to understand the term. In informal speaking and writing, the term is often used more loosely than among professional psychologists.

Solution 2:

subtle TFD

a. So slight as to be difficult to detect or describe; elusive: a subtle smile.

b. Difficult to understand; abstruse:

As in:

The use of (x) has a subtle effect on our mental processes.

Solution 3:

Permeating:

to pass into or through every part of

to be diffused through; pervade; saturate

Solution 4:

In this particular context, I would use subconscious¹. From Oxford Dictionaries:

Of or concerning the part of the mind of which one is not fully aware but which influences one's actions and feelings.

This is a fairly neutral term, and captures the sense of affecting thought processes without the thinker's conscious awareness. It would work adverbially, as well, so you could say either

The use of (x) has a subconscious effect on our mental processes.

Or

The use of (x) subconsciously affects on our mental processes.

If those don't sound strong enough, you could add a modifier (and could potentially drop the phrase "mental processes, since that is implied in the term) for something like

The use of (x) has various/widespread/pervasive subconscious effects.

¹_{Or unconscious if you want to be consistent with technical psychoanalytic terminology. However, in a lay setting I think subconscious is at least as common.}