Lynch liked that method of establishing duality so much that he used it again in Lost Highway. Patricia Arquette plays two roles: Renee, the raven-haired, bored, unfaithful wife of Fred Madison; and also Alice, the platinum blonde porno star who begins a lurid affair with Fred's alter-ego, Pete. Each version of Arquette has strengths and flaws that the other character lacks; the two are polar opposites, yet nearly identical.

In Twin Peaks, Lynch created the notion of the white and black lodges, the former a spiritual place of love, peace and harmony, the latter a place of evil and corruption. In addition, when humans entered the Black Lodge, they met up with their own "doppleganger", or "shadow-self." If people were unable to face their evil twin with perfect courage, the doppleganger annihilated their soul.

Lynch widened the dark/light motif beyond the scope of individuals and applied it to locations. The town of Twin Peaks has a "shadow-self" in Fire Walk With Me -- the town of Deer Meadow. Twin Peaks was a beautiful, placid setting -- people were friendly, the food was delicious, and the air was clean. Deer Meadow, however, was not so idyllic. The police were belligerent and rude (we later find that the deputy is a cocaine dealer), the diner food is rotten, and all the characters we meet live in a dumpy trailer park.

Another theme that Lynch is taken with is the loss of innocence. Jeffrey Beaumont, in Blue Velvet, began the movie as an innocent boy who begins investigating the case of an amputated ear he finds in a field. As the film develops, and he gets involved with shady characters, he finds that he has a darker side: he enjoys voyeurism and rough sex. His loss of innocence culminates in a scene where he reflects upon events of the previous night, and he weeps brokenly at his own actions.

John Merrick, in The Elephant Man, is a sweet, gentle man despite his many hardships. However, he loses part of his innocence one night when a hospital guard brings in a group of drunks to jeer at him. In an emotionally wrenching scene, the marauders pour alcohol into John's mouth, dance him around the room, and hold a mirror to his face. John, for the first time, sees his hideous exterior and screams in self-realization, a knowledge that alters him.

Another theme that Lynch focuses on is abuse and violation, and specifically, the idea that the victims enjoy it. As Laura Palmer is being raped by BOB in Fire Walk With Me, she moans in pleasure. In an audiotape, she later confesses "I think he tried to kill me ... but as you know, I really got off on it." In Wild at Heart, Bobby Peru grabs and fondles Lula while her lover is away, promising to let her go if she whispers "Fuck me." His hand runs over her breast and down to her vagina; as he probes her, her mouth opens in silent ecstasy and her hand slowly opens. In Blue Velvet, Frank brutally slaps Dorothy to the floor. As her head reels, a euphoric smile spreads across her face.

Lynch also has certain character types that appear in many films. "Physically different" characters: the disabled, freaks, physical oddities, etc. appear in all his works. The baby in Eraserhead looks like a cross between a fetus and a lizard. Besides the severely deformed John Merrick in Elephant Man, there are numerous other carnival freaks who help him escape from Bytes. In this film, in fact, Lynch gives the freaks a nobility that many "normal" characters lack. Other "physically different" characters include Grace Zabriskie in Wild at Heart, the one-armed man in Twin Peaks, Double-Ed in Blue Velvet, etc.

The "mysterious" character is also frequently spotted. The lady in the radiator, from Eraserhead, was definitely strange. She appeared to Henry with dreams of heaven -- she was an ideal that he strove for. In Twin Peaks, both the giant and the dwarf appeared from a spiritual realm to give Agent Cooper advice; in addition, the clairvoyant Log Lady lived right in town. And in Lost Highway, the "Mystery Man" appeared to Fred Madison -- it wasn't even clear whether he was trying to help or hinder.

All these odd characters appear to the protagonists; this is typical of Lynch's "bizarre" aspects in his films. This is a further extension of Lynch's dependence and affinity for images; he doesn't care so much whether things make sense, so long as they are beautiful and/or intriguing. As he says:

In Hollywood ... they're making ... stories that are understood by people ... and they become worried if even for one small moment something happens that is not understood by everyone. But what's so fantastic is to get down into areas where things are abstract and where things are felt, or understood in an intuitive way, that you can't put a microphone to somebody at the theatre and say "Did you understand that?" but they come out with a strange fantastic feeling ... (Lynch)

In accordance with this purpose, Lynch often creates situations which are seemingly nonsensical, but evoke powerful feeling. This type of scenario appears in most of his films: in Eraserhead, Henry Spencer enters his radiator, his head falls off, and it falls to the street below where a young boy picks it up. The boy takes Henry's head to a factory where they make erasers out of it. In the next scene, Henry has his head back; it had been a dream, perhaps? Who knows? In Twin Peaks, Agent Cooper has a dream where he enters a red room with a black and white zigzag floor; he meets a dwarf who tells him things like "I've got good news! That gum you like is going to come back in style." Events appear disjointed, yet the scene has a wonderful creepiness to it. Lynch doesn't want the audience to necessarily figure out what it means. As he says, "It makes me uncomfortable to talk about meanings and things. It's better not to know so much about what things mean." (Lynch)

Lynch also has some fun with self-portrayal. The character of Henry Spencer in Eraserhead is Lynch himself. At the time he was creating the film, he was living in Philadelphia and hated it. He also had accidentally fathered a child and got married. In Eraserhead, Henry lives in a dirty, trash filled city; he is forced into marriage when his girlfriend gives birth to a malformed baby. There was even speculation about whether Lynch made Henry's baby a freak because his own daughter (Jennifer Lynch) was born with clubbed feet.

Jeffrey Beaumont, in Blue Velvet, is another depiction of Lynch. Lynch grew up in a logging town in Montana, much like "Lumberton, USA." Jeffrey, like Lynch, is a kind, thoughtful person who discovers that he has one hell of a dark streak.

Perhaps the best (and funniest) self-reference was the character of FBI Agent Gordon Cole, whom Lynch portrayed himself. Cole has an exaggerated version of Lynch's hairstyle, shouts constantly because he's nearly deaf (Lynch is considered a very loud-spoken person); and has a "code." In Fire Walk With Me, Cole delivers an agent's assignment through a woman named Lil, who performs a complicated little dance. The agent must dissect the meaning of Cole's code, just as viewers often have to dissect the meaning of Lynch's symbolism.