You've checked your shakes or shingles, looked for pooled water, and your roof is still leaking. It might be time to inspect other areas on your roof that often cause leaks -- open roof valleys and flashing.
Open Roof Valleys
To repair an open valley:
Step 1: Inspect valley for holes all along joint. You can patch small holes with the same type of sheet metal valley is made of. Most valleys use either aluminum or copper. Using different metal to patch valley will cause corrosion.
Step 2: Clean surface of valley with wire brush.
Step 3: Cut sheet metal patch about 2 inches bigger all around than hole.
Step 4: Spread thick coating of roof cement on damaged area and press patch into place, bending it to shape of valley. Spread more roof cement over edges of patch to seal out water.