1) A friendly enquiry about the health of one's paternal relative.
2) A phrase to use when you've temporarily lost the right word. Or want to hide that word in order to shield more delicate ears.
3) Sexual intercourse or similar intimate entertainment requiring euphemistic reference. Accompanied by winking and smiling.
2) *indignant* Well that's a fine how's-yer-father, in't it?
3) We had a lovely picnic, got pleasantly drunk, then spent the whole afternoon in lazy, sunny how's-yer-father.