Extra innings count for settlement unless the market says otherwise. This includes Moneyline, Run Line, Total Runs, and Last Team to Score markets.
For example: a game is tied after 9 innings, and the home team wins 5-4 in the 10th. A Moneyline bet on the home team wins, and an Over 8.5 Total Runs bet also wins because the final score is counted.
For more information, see the General Rules, Tickets & Wagers article.