Paul did have a car crash on November 9, 1966, the day John first met Yoko Ono. John's close friend Tara Browne, aged 21, did die in that crash.
VISIBLE SIGNS:
Sgt. Pepper's Lonely Hearts Club Band (1967):
John, George, and ringo hold gold instruments, but Paul holds a black instrument. The black is sometimes a symbol of death in some cultures.
Magical Mystery Tour (1967):
The black walrus is a sign of death in some parts of Scandinavia.
Paul holds his hand above his head, which is a possible sign of death.
In the film, Paul wears a black carnation, while the others wear red.
Abbey Road (1969):
Paul walks barefoot in a "funeral procession", holds a cigarette in his right hand, and the license plate on the white Volkswagen reads "28IF", supposedly Paul's age "if he had lived" (Paul was only 27 when the album was released).
INVISIBLE SIGNS:
"Strawberry Fields Forever" (1967): John is interpreted to have said, "I buried Paul", though he actually said, "Cranberry sauce".
"A Day in the Life" (Sgt. Pepper): "He blew his mind out in a car"
"I am the Walrus" (Magical Mystery Tour): Shakespearean actors say at the end of this song, "What is he dead", "Bury my body", and "O, untimely death".
"Glass Onion" (The Beatles [The White Album], 1968): "The walrus was Paul"
"While My Guitar Gently Weeps": George is sometimes interpreted as singing "Paul, Paul" as if he misses the dead man.
Between "I'm So Tired" and "Blackbird" (White): When John's nonsense syllables are played backwards, they supposedly say, "Paul is dead, man, miss him, miss him".