IN

Use 'in' with spaces:

in a room / in a building

in a garden / in a park

Use 'in' with bodies of water:

in the water

in the sea

in a river

Use 'in' with lines:

in a row / in a line

in a queue

Use 'in' with cars and taxis:

She is in the car / taxi.

AT

Use 'at' with places:

at the bus-stop

at the door

at the cinema

at the end of the street

Use 'at' with places on a page:

at the top of the page

at the bottom of the page

Use 'at' in groups of people:

at the back of the class

at the front of the class

ON

Use 'on' with surfaces:

on the ceiling / on the wall / on the floor

on the table

Use 'on' with small islands and beaches:

I stayed on Maui.

She is on the beach.

Use 'on' with directions:

on the left

on the right

straight on

Use 'on' with means of transportation:

They are on the bus / train /place / subway.

NOTE:  We also say on foot. She came home on foot.

IMPORTANT NOTES

In / at / on the corner

We say 'in the corner of a room', but 'at the corner (or 'on the corner') of a street'

In / at / on the front

We say 'in the front / in the back' of a car

We say 'at the front / at the back' of buildings / groups of people

We say 'on the front / on the back' of a piece of paper