Check both sides of rafters because water may run down them to the wall. Look carefully around all vent pipes going through the roof and around the chimney, if you have one. When the rain stops, inspect the roof from the ground with a pair of binoculars. If you feel comfortable, go on the roof, but wear proper fall restraint equipment. Look for missing shingles or water pooling in certain areas.
Leaks often begin around flashing or where two roofs join, particularly if one was added on later.
If the valley is clogged with leaves, water can back up beyond the valley flashing and penetrate the roof. This can also happen if the valley is too narrow for the amount of water running down it. You can sometimes narrow the search by running a hose over the suspect area to see if the leak resumes. If it is a leak during winter in cold climates, ice dams along the eaves can force melting snow to back up under the shingles and into the house. Converting a flat roof to a pitched roof is a major undertaking that requires skilled carpenters and roofers.