Flight, and what it costs
Flying is the studio's most obvious motif and its least sentimental one. Kiki loses the ability to fly and has to sit with that. Porco flies because he cannot bear the company of people. The Wind Rises is about a man whose beautiful designs are handed to a war ministry. Even Castle in the Sky, the most straightforwardly joyful of the flying films, ends with the flying thing being destroyed on purpose.
What the films seem to argue is that flight is freedom and freedom has a bill attached. That is a strange message for a studio whose merchandise is full of aircraft, and the tension is not accidental.
Food, cooked in real time
Ghibli food scenes are famous, and the reason they work is that they are animated at the speed cooking actually happens. Bacon spits for as long as bacon spits. Bread is torn, not bitten. The ramen in Ponyo takes the full length of time it takes noodles to soften under a lid.
Two functions. First, food establishes that a world is physically real, which matters enormously when the next scene contains a spirit. Second, in almost every case, someone is feeding someone else — it is the studio's standard shorthand for care that nobody has to announce out loud.
Work as the actual subject
An unusual number of these films are about jobs. Kiki runs a delivery business and experiences burnout. Chihiro's arc is a work story: she is given a contract, a new name, and a shift scrubbing a filthy tub. Shōta pilots a train because it is his route. The bathhouse in Spirited Away is drawn as a workplace with hierarchies, break rooms and a terrible boss.
American animation of the same period tended to treat work as an obstacle to a dream. Ghibli treats competence at ordinary work as a form of dignity, and treats losing your name to your employer as the thing to be afraid of.
Weather that has opinions
Rain in these films is not a mood filter; it has temperature, volume and consequences. The famous bus stop scene in Totoro works because you know how cold the girls are. Storms in Ponyo are drawn with a nearly abstract fury that no other studio would attempt by hand.
This connects to background painting practice: weather is where the art department is allowed to take over the frame, and the animators plan for it.
Antagonists who are not villains
This is the hardest adjustment for a viewer raised on American animation, and the most rewarding one. Princess Mononoke is the clearest case. Lady Eboshi is deforesting a mountain and killing a god. She is also employing lepers and former brothel workers who had nowhere else to go, and treating them decently. The film refuses to resolve this.
Even where a character is straightforwardly hostile — Yubaba, Muska, the Count — the ending is rarely punitive. Characters are outlasted, or absorbed, or persuaded, or simply left behind. Very few Ghibli films end with a defeated enemy on the floor.
A story where the opposition is reasonable is much harder to write and much harder to end. Ghibli keeps choosing it anyway.
Protagonists who are girls, and are not prizes
Across the catalogue the lead is usually a girl between ten and eighteen, and she is almost never the object of a romance plot. She has a task, or a job, or a journey. Where romance appears it is quiet and usually secondary to a decision she makes about her own work — Whisper of the Heart is a love story in which the actual drama is whether she can finish writing something.
Trains, and going somewhere without a destination
The train sequence in Spirited Away. The tram in Whisper of the Heart. The commuter trains of Only Yesterday and Poppy Hill. Ghibli likes vehicles you cannot steer, and it uses them for the same purpose every time: a stretch of the film where the character can do nothing but sit, and the audience is invited to sit with them.
Ruins, gardens, and things growing back
The last pattern is the most hopeful. Nature in these films is not fragile scenery; it is patient and slightly indifferent. Laputa is being taken apart by its own roots. The valley of Nausicaä is being cleaned by a forest that happens to be lethal to humans, which is not the forest's problem. The films worry about people, and are relatively relaxed about the planet.