When it is raining, inspect your roof from outside and from within the attic. From the attic, look to see if you can see daylight through holes cut into the sheathing, water stains, or water droplets. From the exterior, look up from the ground to see how water runs down off the roof. No pooling of water should be evident and gutters should be moving water flow away from the roof and foundation. Also, look for shingle deterioration or other roofing damage. Inspect the soffit, louver, and ridge vents closely for signs of infiltration in high winds. Gable end wall louvers should be permanently closed off if your home is in a hurricane area, or temporarily boarded up before each storm.
Evidence of water stains is usually the first indication that water is coming into the house from the roof. The stain could be on the roof sheathing, the insulation, or even the drywall of the ceiling below. Water will travel a path of least resistance, often leaving a stain far from where it first penetrated. It usually takes several inspections to pinpoint the source of a leak seen from within the home.
Repairing roof flashing can be as simple as replacing a pipe collar rotted by the sun to a whole house shingle tear-off and reroof due to extensive infiltration at step flashing that has not been inspected and maintained. Be sure to inspect the roof periodically, and tape joints while performing the repair.