What determines in which direction a runway is used?
There are several factors:


Prevailing winds
Neighboring airport traffic patterns
Size of inbound aircraft
Where the aircraft is coming from
Final parking space
Congestion
Fuel status
Weather (thunderstorms)
Noise considerations


At small airports, it is usually just the runway that faces into the wind and can accommodate most of the traffic coming in.

At large airports, the wind dictates which flow is being used (like a "north flow" or "south flow"). From there, aircraft usually are assigned to land on which ever side of the airport their arrival procedure brings them to. Sometimes, it is also decided by which gate/terminal they'll be parking at. Lastly, the available approach procedures can change things if the weather is not good