I hired a guy to replace a rotting deck to a rental unit above my home. He didn't, and I sued him in small claims. He refused to pay. Do I write his invoice off?

Since you were not reimbursed you can deduct what you paid as an expense. 

What you paid for the repair is a valid rental expense, weather the repair was actually done or not. Additionally, any legal expenses you incurred in this matter are also deductible as a rental expense. If I recall, there's a line item on SCH E for Legal and Professional Fees where you can claim your costs associated with small claims.