They obviously have a ton of these. Some subtle ones:

In terms of song structure....the coda or outro in 'Ticket to Ride'. Wasn't a traditional technique in pop music until they did it.

Tons of subtle production techniques that we can probably mostly attribute to George Martin:

The saturation/distortion on the vocals in 'I am The Walrus'.

The use of 'backwards' playback on the guitar for 'I'm only sleeping'.

The phasing effect on Lennon's vocal for 'Across the Universe'. Similarly, on 'Tomorrow never knows' they put the vocal through a Leslie cabinet.