In general, 'on' is short for on top of a surface, 'in' is short for inside of a structure, and 'at' means a point in space or time.
1. We want to start the meeting on time, so please don t be late.
==> Time = numbers; numbers are on the surface of a clock's face. 'on time' is an idiom meaning punctual, not late.
2. Where is the car waiting? Atthe traffic lights.
==> Location = a point in space; the car is not sitting on top of the traffic lights.
3. The leaves onthat tree are a beautiful color.
==> The leaves are located on the branches of the tree.
4. He spends most of the day sitting atthe window and looking outside.
==> Location = a point in space; he is not sitting on top of the window.
5. I like that picture hanging on the wall inthe kitchen.
==> The kitchen is a 3 dimentional space. It is a room, a structure. It has an inside, so use 'in(side)' the kitchen.
All the best,