Finding the entry point
A leak shows up inside at the low point of wherever the water traveled along a rafter or across the top of a ceiling. Going up and patching the shingles directly above the stain fixes nothing. I start in the attic on the day of a rain if I can, or with a hose on the roof if I cannot, and trace the water back along the framing to the spot where it comes through the deck. Then I go up and look at what is above that spot.
It is usually one of a handful of things: a flashing failure at a chimney, plumbing vent, or wall; a nail that backed out and lifted a shingle; a cracked or missing shingle from wind; a valley where the shingles were cut wrong; or a rubber seam that has opened on a porch roof.
Flashing repairs
Chimneys are the number one source. Springfield's brick chimneys were flashed in lead or copper a century ago and re-flashed with roofing cement every decade since. Roofing cement is a temporary patch that fails in a few seasons of freeze-thaw. The proper repair is new step flashing woven with the shingles and new counterflashing cut into the mortar joints. Plumbing vents get new rubber boots when the old ones crack in the sun. Wall intersections get new step flashing and kickouts, which means lifting a few courses of siding.
Shingle repairs
Individual architectural shingles can be replaced by breaking the seal on the courses above, pulling the nails, sliding a new shingle in, and re-nailing under the course above. It is careful work in cold weather because the shingles are brittle, which is why I do shingle repairs on a mild day or warm the shingles first. A repair that cracks the neighboring shingles has created three leaks to fix one.
Where wind has lifted a whole section, I check that the nails in the surrounding area are still holding before I re-seal, since wind damage often means the nails were placed too high in the first place.
Rubber roof repairs
EPDM on a porch or addition roof fails at the seams and the edges. A repair is a cleaned and primed patch with proper seam tape, or a new termination bar and edge metal where the edge has lifted. Rolled asphalt roofs are usually not worth repairing because the material itself has reached the end of its life, and I will say so rather than sell a patch that will not hold.
When a repair is not the answer
If I get up there and find a roof with widespread cracked shingles, exposed nail heads across the whole slope, and rotted decking that I can feel underfoot, I will tell you that a repair would be throwing money at a roof that needs to be replaced. I would rather lose the small job than take it and have you call me again in the spring.
Repairs after a storm
After a summer thunderstorm or a heavy wind event, I look at the whole roof, not just the obvious damage. Hail bruises that will not leak for a year, lifted shingles that have lost their seal, and debris in a valley all need attention. I write it up in a way that is useful if you are making a claim, with photos, and I tarp anything that is open until the repair is done.