roof leaking in the rainy season can drive you crazy but here a 5 place on your roof where the problem could be coming from. check all of these five places and you'll find the problem and you can tarp or gloop up the problem
chimney is definitely one of the first places I would check if the water spots appear near the chimney place. Warn out counter flashing or no counter flashing at all can cause water to run directly down your chimney and into the attic. Sometimes this happens right after a new roof is installed and the old roof is ripped away and old gloop separated. When the new roof runs up to the chimney and there is no counter flashing to protect the attic. The chimney cap or mortar can be cracked or just warn away, the holes appear and as a result the chimney is barrelling or falling apart.
Skylight leaks happen generally when the skylight turns 20 years old and moss accumulates on the top end of the skylight. the rains come and actually dam up forcing the water up against gravity and up the flashing and into your home. seals can expire where the glass meets the frame but this does not happen to often
plumbing stacks, B Vent, roof vents and goose necks leak when the nails that holed them down rust and break apart tiny holes and leak. This generally happens when your shingles outlived the flashing. this is a good thing, if this is your situation it is time to change and be happy you had a good innings
capping which runs along the top and down the hips of the roof wear away due to the fact that they are horizontally facing the elements. cedar shake it the victim of the caps breaking apart early or split early. this is the one spot where replacement of capping without shingles is possible
valley's are notorious weak spots only because there is no other spot on your roof where more water runs in one area. ice and snow accumulates in these area of the roof so getting a metal valley is probably the best recommendation
if all else fails the best is to run a trap along the ridge of the roof, the ridge being the highest point and blanket it over the side of the roof which is leaking. This is the best method of protecting the interior of your home and allowing you to decide of what to do from there