Many people are familiar with Koishi's ability to "manipulate the subconscious," yet usually they are imagining something completely different than what it actually is! Her ability isn't as straightforward as being able to manipulate psychological concepts like the Id or Super-Ego; instead, Koishi has been shown to be manifesting other things, such as abstract symbols, her own mind, and consciousness. This post is mean to provide a detailed overview on the variety of ways Koishi's ability is demonstrated throughout the series, and also provide a comprehensive theory surrounding her issues with memory, one of the most enigmatic parts of her character.
Koishi's most vivid demonstration of her ability lies in it's manifestation of concepts brought to life in the form of danmaku. As when know from an earlier ZUN Interview (1), the first word outside of quotations in the spellcard is the "type" or "genre" of attack, and the part in quotations is the name. In game, Koishi's primary type of attack is the word 表象 (hyoushou), which has been translated in a variety of different names. Using weblio for a definition, it describes it as being a symbol of something abstract, a symbolic representation. In terms of philosophy and psychology, the word is what we call the intuitive images inside your mind that are produced when thinking of external objects. At first it was translated as "Symbol," but then later changed to "Representation" and the current "Image."
I'm going to be honest with you guys, I am REALLY pissed that they changed it to "Image," and changing it to "Representation" was just absurd. "Symbol" made immediate and clear sense, and also sounds way cooler. I think "Symbol" and "Image" are essentially synonymous in this context and that there are way bigger issues with modern translations that people should be occupying themselves with.

Regardless, Koishi seems very aware of what this facet of her ability entails. In Subterranean Animism, she describes it as, "The danmaku that lurk in your unconscious are the danmaku that my sister has never seen!" (2) and she has been described as awakening or evoking the things that you are unconsciously thinking about (3). Marisa writes that Koishi's spellcard, Symbol 'Danmaku Paranoia,' is a card that reaches deep into the recesses of your mind to call forth vague images. We also know that another spellcard, Embyro's Dream, is meant to my symbolically representative of the memories of all life, as explained by Koishi. (4)
So regardless of what exactly you what to call it, the primary usage of Koishi's ability seems to manifest images and symbolic concepts--the vague ones that exist in the depths of your subconscious, as well as anything you might be unconsciously preoccupied with.
The other most common usage of Koishi's ability is not focusing on the mind of her opponent, but rather her own. Multiple times within canon work, Koishi is shown to have an almost telepathic or synchronous relationship to her opponent's mind, and by altering her own mind she is able to influence her opponent's. Additionally, any change or fluctuation in Koishi's mind can become physically manifested in battle, typically in the form of danmaku.
One of Koishi's skillcards, Conditioned Teleport, is described as "An intimidating move where Koishi sneaks up to her opponent as her consciousness reaches them...The area that Koishi's consciousness can cover becomes larger with time, but conversely, she can't hold herself back from attacking any opponent within that range." (5) In this example we see a mental facet of Koishi (her consciousness) becoming physically materialized, functioning as the range of her surprise attack. Another example is Growing Pain, where her consciousness takes upon the form of a rose vine that is reflexively directed outward towards the opponent. Another example is found in Reflex Radar, which says that her mind produces a "tracing thought wave" that tracks the opponent down, linking it to an instant attack.
From the above examples, it's now obvious that Koishi's psyche itself can become manifest in the battle field. But what about the effect it apparently has on her opponent? This is one of the most surprising facets of her ability; depending on what is happening in Koishi's psyche, her opponent is influenced. One example of this is the skillcard Stinging Mind, which reads, "Koishi covers the surrounding area in rose mines, but promptly forgets about their presence. Due to her influence, the opponent, too, becomes unable to recognize any of the mines besides those nearby." (5) This description suggests that it is because Koishi herself forgets the attack, that so does her opponent.
Two more key examples come in the form of her classic spellcards, Instinct 'Release of the Id' and Suppression 'Super-Ego'. The first describes Koishi opening her mind as much as possible and the opponent unconsciously distancing themselves due to the aftershock of her emotions. The latter reads, "She suppresses her mind as much as possible. The aftershock from it deals damage in the area around Koishi, and due to her influence, the opponent unconsciously gets closer to her." (5) As Koishi opens and suppresses her heart, it creates a palpable aftershock that impacts the opponent on an unconscious level, resulting in changes to their physical movement and position.

We even see this component of her ability demonstrated in her spellcard Philosophy of the Hated Person, which is described by Marisa as, "A unique Spell Card where only the danmaku in Koishi's vicinity becomes thorny. By closing her heart even further, she makes it impossible to see anything but the danmaku, let alone herself." (3) Marisa attributes the cause--Koishi closing her own heart--with an effect inflicted upon the opponent, that of being a loss of visibility. This also might explain why during this spellcard in game, the scrolling background disappears and is replaced by total darkness.
For the same of a quick summary, we know that Koishi can affect the opponent's:
❥Physical Movement and Positioning
❥Memory
❥Vision
And Koishi can do so by:
❥Opening and suppressing her own mind
❥Forgetting her own memory of something
❥Closing her heart
It's very probable that there lie many more potential ways Koishi can use this part of her ability, but these are the only things I could find that are directly referenced in canon material!
In the game Hopeless Masquerade, Koishi's special skill is described as "Super-Responsive Senses," (6) yet we've seen a similar concept associated with her in previous games. In SA, the word 反応 (hannou) is another type of spellcard in her arsenal, which means "reaction" or "response." Unfortunately, the description of Koishi's special skill is focused mostly on the in-game mechanics of it and potential player strategies. The only in-universe detail we receive that Koishi's senses far surpass human limitations. That being said, it's very reasonable to conclude that several of Koishi's attacks in-game are using this facet of her ability in some way, so we can examine them to learn a little more.
Found many times in Koishi's attacks is a sense of inability to hold back, or a lack of complete control. We saw in Conditioned Teleport that Koishi manifests the attack herself, but once the opponent enters her range it becomes involuntary. Another skillcard named Fidgety Snatcher states that it is a move where she reflexively lunges at anybody close by, and Growing Pain is not an intentional attack, "but one that occurs when she remembers it in the corner of her mind." (5) One last example includes the card Catch and Rose, which is where Koishi is unable to repress her desire of wanting to catch the opponent, and so she shoots out her hands and the attack begins.

The range of intentionality seems to vary greatly in these attacks. Some of her attacks are deliberate, but also contain an uncontrollable, reflexive element that is triggered by environmental conditions. In general, Koishi's reflexes seem to depend on her own sense of the opponent, such as their position or presence, but also can become activated by her own impulses and feelings if she cannot suppress them. Some attacks also seem to be triggered by her own mental facilities, such her remembering something or becoming curious about the opponent. Koishi herself is aware of this, and states directly in game that she believes it to be better to fight by your own instincts during battle. (7)

The contradiction of Koishi remembering some details, but not others, is explained. She remembers what occurs during states of consciousness, and forgets anything that happens while unconscious.
It does not violate or contradict any canon detail we have about Koishi's memory loss. Under this framework, Koishi would still "remember nothing" and likely experience this everyday, as it happens anytime she decides to act unconsciously.
It explains with Koishi's dialogue line, where she states she she always forgets things right after doing them. We know that Koishi makes the decision to go to the shrine and that she remembers her want to in the first place--yet under this framework, that would be all that she remembers. She would remember the "before" and "after," but not the "during," the actual process of preforming the action. From her perspective, she would decide to act, black out, and then "wake up" having already completed the action--thus, forgetting things right after doing them.
❥(1) Strange Creators of Outer World’s FAQ about the Spell Card System
❥(2) Reimu and Suika’s Extra
❥(3) Koishi’s Spell-Cards in The Grimoire of Marisa
❥(4) The Grimoire of Usami/Section 2-3
❥(5) Koishi’s Spell-Cards in Hopeless Masquerade
❥(6) Koishi’s Official Profile on the website for the game Hopeless Masquerade
❥(7) Koishi’s Script in Hopeless Masquerade
❥(8) Koishi’s Official Profile in the omake.txt file from Subterranean Animism
❥(9) Satori and Koishi's article from Who's Who of Humans & Youkai in Gensokyo
❥(10) Marisa and Patchouli’s Extra
❥(11) Toyosatomimi no Miko and Byakuren Hijiri's Scenario in Antinomy of Common Flowers