I'd take it like this: Something(S) + comes (Vi) + in (Adverb) + handy (Adjective functioning as subject complement). So it has essentially the same structure as "It looks good", "That sounds right", etc. If I recall correctly what I learned from high school grammar book, there are five sentence patterns in English, as shown. "come in handy" belongs to the #4 pattern. 1. S + V-i "I exist" (S=subject, V-i=intransitive verb). 2. S + V-t + O "I love you" (V-t=transitive verb, O=object). 3. S + V-t + O-i + O-d "I sent him a letter" (O-i=indirect object, O-d=direct object). 4. S + V-i + C-s "I am a student", "It looks good" (C-s=subject complement). 5. S + V-t + O + C-o "He knocked me unconscious" (C-o=object complement).

It's just a fixed expression. Offhand, I can't really think of any similar phrases. If we really want to analyze the structure, I'd say "handy" is probably an adjective, being used as a predicate nominative.

These paper plates should come in handy on your camping trip. I'm glad I took an umbrella. It really came in handy when it began to rain. Take this jacket with you. It could come in handy if the weather changes.