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All the goodness of Mind Rape... with the bitter aftertaste!
When somebody is Brainwashed and gets better, but somehow part of the programming sticks and it shows by the character acquiring new personality traits, tics and/or quirks. For example, Alice is a mind controller who casts a spell on Bob to make him fall in love with her. Bob somehow breaks the spell, but whenever he looks at Alice now, he blushes and can't quite explain why. Maybe he's falling in love for real, but who knows for sure.
This can be used as a Plot Device to show that the character hasn't quite fully-recovered from his brainwashing. Maybe he has, but the idea of being somebody Not Himself makes him change... probably for the better. Can become a Family-Unfriendly Aesop when brainwashing is the only way for a character to change.
Also comes in other flavors:
Laser-Guided Amnesia-flavor: Either by magic or any other mind-altering means (Time Travel, Reset Button, etc.). Alice makes Bob forget that he was ever in love with her, but somehow Bob still retains faint, lingering sentiments for her.
Compare and contrast with More Than Mind Control, where the character more or less knows that he is/was being manipulated, but goes along anyway. See Cartesian Karma for when the residue may or may not have resided, but the consequences of their brain-washed actions are still quite valid.
In ROD the TV, Anita becomes a bookworm like her sisters after she gets a part of The Gentleman's memories. Take note, Anita used to hate books.
Or perhaps she just got a better understanding of Yomiko Readman and books in general.
All of the girls Keima "conquers" in The World God Only Knows show signs of this. They just can't explain why they blush whenever the geeky otaku walks by.
Gundam SEED Destiny has Stella, an Earth Alliance Extended who is brainwashed so she freezes up whenever anyone says "die" and absolutely trusts anyone who says "protect". Due to her memories not being properly wiped between missions, her programming leads her to associate Shinn with protection, thus allowing her to remember who he is.
Neo Roanoke has the amnesia-type: his original identity, that of Mu La Flaga, begins to re-emerge after he's brought aboard the Archangel. He finds Murrue inexplicably familiar, instinctively remembers the ship's communication codes, and eventually begins experiencing flashes of Mu's memories and using his old Catch Phrase.
In the manga of Kenichi: The Mightiest Disciple, Miu, a kind hearted talented martial artist girl, gets captured by the Blood KnightEvil Mentor Silkwat Junazard and gets a combination of amnesia and brainwashing which conditioned her to extreme aggression and bloodlust. Even upon being rescued and her memory restored, her bloodlust and aggression still lies subconsciously, often triggering when her emotions run high or when exerting significant effort in martial arts, even during a simple and safe training exercise. Part of this is because the bloodlust and aggression had always been a part of Miu. It's the main reason Junazard wanted her to be his disciple in the first place. Miu's grandfather trained her from an early age specifically to help her control it.
TRON fanon often plays this up in post-TRON: Legacy scenarios with Tron and that Rinzler programming. The residue ranges from massiveguilt issues, VerbalTics, bizarre thought patterns, or even fits of madness where he attacks his allies.
In G.I. Joe, the Baroness is kept under supervision because they can't remove the mind-controlling nanomites just yet. Prior to that, she is shown to have retained some of her "training" by being able to operate a gun pod.
The main plot point of Inception uses a planted "idea" to change a person's outlook in life. This could be for the better (Robert Fischer views his father in a better light and avoids a possible energy monopoly with his company) or worse (Mal commits suicide thinking the reality she's living in is still a dream).
Total Recall (1990). After Quaid breaks Melina out of the constraints one of the Recall machines, it seems just a bit of the Housewife programming made it though, but not by much.
The Shapeshifting flavor happens in Discworld, although it isn't involuntary, and Granny Weatherwax only "Borrows" an animal's body for some purpose, sharing it with the real animal for a short time. But after she's exited the animal's body, she still retains impulses from whatever shape she borrowed. For example, she stopped using owls to see at night because "You ends up for days trying to twist your head right round," and after she's borrowed an entire beehive, she declares, "I wantzzz a bunzzch of flowerzz, a pot of honey, and someone to szzzting."
It's also noted that at least one of the people she made think they had been turned into a frog still enjoy swimming in a pond long after the spell wore off. He was grateful for getting a new hobby.
In the Deryni works, Sean Lord Derry suffers from this, referring to nightmares he had after his captivity and torture at the hands of Wencit of Torenth. He reluctantly admits the nightmares returned years later in anticipation of Kelson's trip to Torenth for Liam-Lajos's investiture in King Kelson's Bride. This foreshadows Morag's reasserting control over his mind, control which is taken and used by Teymuraz.
In the New Jedi Order, after Tahiri is rescued from an attempt to brainwash her into believing she was a Yuuzhan Vong, it became a running subplot for several books that she retained most of the false memories subconsciously and under moments of extreme stress would adopt Vong mannerisms or even spout the Vong language. It was eventually revealed that the brainwashing had failed to overwrite Tahiri's original personality but had succeeded in creating a Yuuzhan Vong personality, Riina, who was almost totally independent of Tahiri's own mind. They ended up combining into a third personality to avoid going incurably insane.
Happens in Warehouse13 after Leena is saved from being brainwashed by McPhearson.
In an episode of Star Trek: The Next Generation, Lt. Barclay got a brain upgrade by some aliens, which went away after it was needed. He and Troi were in Ten-Forward and he saw a Chess game, moved a piece and said "Checkmate in three moves."
Troi: "Reg, I didn't know you play chess."
Barclay: "I don't."
Crichton from Farscape has Scorpius residue for ages after getting his chip removed (overlaps with Imaginary Enemy).
In the original V miniseries, Diana has attempted to brainwash Julie Parish into being her slave. She fights off the brainwashing, mostly successfully, but occasionally catches herself using the wrong hand. In V: The Final Battle, Diana telepathically commands Julie and she has flashbacks to the brainwashing. Julie doesn't quite give in, but the internal struggle gives Diana a chance to escape.
Also, after Dracula Renfield-ised Xander in season five, Xander still referred to Dracula as "Master" several episodes later and in the Season 8 comics.
Falling Skies has a lot of this with the rescued teens. The harnesses are removed, but the spikes can't be removed without killing the kids. Between that and the unknown effects of the ordeal, Ben, Karen, and a few others are experiencing this.
In Kingdom Hearts II, when Sora bids farewell to Hayner, Pence and Olette, he sheds a single tear but doesn't know why. Little does he know that he has Roxas' memories within him, and he remembers them as his friends in the virtual world.
NieR decides to save Kainé at the cost of his own existence in the final ending. When she comes to, she starts crying when she finds the flower Nier gave her, but can't remember who it was from.
In The King of Fighters, Ash sacrifices his existence to prevent the entire Ash Saga from happening. None of the other characters remember him, except for Elizabeth, due to having his Tragic Keepsake.
Final Fantasy VII: Even after Cloud, who absorbed and/or assimilated Zack's memories, regains his real memories, he retains Zack's fighting style and some of his mannerisms. Although he reverts to his real personality and becomes more comfortable with showing his insecurities, he occasionally still puts on Zack's cocky act in front of the others.
Funnily enough Call of Duty: Black Ops plays with some brainwash residue. When Mason escapes from the Soviet Union and gets back to the US, he experiences flashes, seeing and hearing numbers, seeing a hallucination of Reznov despite him being dead and even what looks like scenes of drawing a gun on the president, really the brainwashing hasn't worn off yet.
This extends to Call of Duty: Black Ops 2 - at the end of the second 1980s level, Mason encounters Lev Kravchenko, previously presumed dead in Vietnam. During the next scene, he has to actively suppress an urge to execute him on the spot so that Woods can get some useful information out of him.
In Chapter 34 of Gunnerkrigg CourtJack claims to be in love with Zimmy, and attributes it to a remnant of his possession by a ghostly spider obsessed with Zimmy which tried to take control of his mind. This doesn't seem to worry him.
In Squid Ops, main character Mui brainwashes her sister using some hypnotic squid ink (yes, It Makes Sense in Context) that makes people obedient to her. The first thing she tells her to do is to answer with "Yes, Mui. I obey." whenever Mui gives her a command. Later, after the effects of the ink wear off, Mui brings her sister some lunch and says "Take it and don't be mad, okay?" Lena reflexively replies "Yes, Mui. I obey."
In Ben 10: Alien Force, Albedo is an villain who copied Ben's appearance and Omnitrix. He also gained some of Ben's characteristics, like eating junk food. After having his Omnitrix broken, stuck with Ben's color-swapped form, and taken to prison, he shouts, "BRING ME CHILI FRIES!!!"
In Batman Beyond: Return of the Joker, Tim Drake still has aftereffects of his last encounter with The Joker (of the 'uncontrollable shaking and bad dreams' kind) after 40 years. Given what The Joker put him through, that's really not that surprising.