Coming in handy means it is convenient to have the thing or skills which really help us in time. Some tools or skills thus often offer unexpected helps in tough situations and thus they come in handy.
1) I'm glad you brought your knife." Reply: "Yes, it really comes in handy."
2) Having your dog with us on this hunting trip really came in handy.
3) Speaking Spanish really comes in handy.
4) I carry a pen and paper at all times. They really come in handy.