Tools | Serial Port menu is not visible

If you're using a USB Arduino board, make sure you have installed all the required drivers.

Make sure that the board is plugged in: the serial port menu refreshes whenever you open the Tools menu, so if you just unplugged the board, it won't be in the menu.

Check that you're not running any programs that scan all serial ports, such as PDA sync applications, Bluetooth USB drivers (for example, BlueSoleil), virtual daemon tools, and so on.

On Windows, the COM port assigned to the board may be too high. As described in Zeveland:

On the Mac, if you have an old version of the FTDI drivers, you may need to remove them and reinstall the latest version:

gnu.io.PortInUseException on Mac

Error inside Serial.<init>()
gnu.io.PortInUseException: Unknown
Application
at gnu.io.CommPortIdentifier.open
  (CommPortIdentifier.java:354)
at processing.app.Serial.<init>
  (Serial.java:127)
at processing.app.Serial.<init>(Serial...