It depends on the sport and the market. Here's a breakdown by sport.
Soccer
Most soccer markets are settled on 90 minutes of regular time only—extra time and penalty shootouts do not count unless the market explicitly states otherwise.
Markets that do include extra time will say so explicitly—for example, "To Lift the Trophy" or "Tournament Winner" markets in knockout competitions account for the full result, including extra time.
Basketball
Basketball bets include overtime unless the market states "regular time only."
American football
Bets include overtime unless the market states "regular time only."
Ice hockey
Standard markets are settled on 60 minutes of regular time only. Overtime and shootouts do not count unless the market explicitly includes them.