Plumbing vent pipes (the ones with the rubber collars)
Those bare pipes are your plumbing system's breathers. Each is sealed with a pipe boot: a metal or plastic base flashed into the shingles, with a rubber gasket hugging the pipe. The flashing typically outlives the roof; the rubber doesn't. Sun and weather crack the gasket somewhere past the ten-year mark, and water follows the pipe into the house.
Cracked boots are one of the most common leak sources we repair, and one of the cheapest, which makes them the poster child for catching problems during inspections instead of after ceilings stain.
Exhaust vents: bathroom fans, kitchen hoods, dryers
These are the hooded or capped vents that carry moist indoor air outside. The roof side is straightforward: a flashed cap with a flapper or screen. The failures are usually either aged sealant at the flange or, surprisingly often, the duct underneath was never actually connected, dumping shower steam straight into the attic.
That last one masquerades as a roof problem (damp deck, attic moisture) while being an HVAC problem. (Ventilation and condensation impostors, covered here.)
Flues and chimneys: the hot and the heavy
Furnace and water heater flues get high-temperature flashing assemblies built for metal venting hot exhaust; they're reliable when installed right and unforgiving when improvised.
Masonry chimneys are the heavyweight penetration: wide enough to dam water on their uphill side (bigger ones get a small diverter roof called a cricket), and sealed with the two-part step-and-counter flashing system that's the most common leak source on the whole roof. If your home has a chimney, its flashing deserves a look on every inspection.
Skylights, mounts, and everything else
Skylights are penetrations large enough to earn their own guide: four sides of flashing, factory seals, and a debris-collecting uphill edge.
Then there's the aftermarket: satellite dishes, solar mounts, holiday-light anchors. The rule for anything that pierces the roof after installation day is simple: flashed and sealed properly or not at all. Lag bolts with a squirt of caulk are future leaks, and they can void warranty coverage on the affected area. Looping your roofer in before mounting anything costs a phone call.
During replacements, every penetration gets new flashing and boots as standard; reusing the old ones is a corner we don't cut.
