1. I WILL have cleaned the house by the time my parents come home. (future perfect; happening before another event in the future, i.e., your parents coming home)
2. I have [already] cleaned the house. (present perfect; action continues into present or just completed)
3. I have the house clean by the time my parents come home. (simple present; habitual activity) "Clean" is being used as an adjective here. It describes the condition of the house.