The lower parts of San Juan besides Santa Mesa floods. Streets such as Blumentritt in San Juan can have floods as high as your waist. Gilmore in New Manila would also have portions where it floods. On Tomas Morato, there is a portion where it dips and it always floods there.
Edsa contrary to popular belief alsohas a portion that floods. This is the area close to P Tuazon in QC if I'm not mistaken.