Why doesn't my board show in the Tools | Serial Port menu ?
If you're using a USB Arduino board, make sure you installed the FTDI drivers (see the Howto for directions). If you're using a USB-to-Serial adapter with a serial board, make sure you installed its 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, like PDA sync applications, Bluetooth-USB drivers (e.g. BlueSoleil), virtual daemon tools, etc.
On Windows, the COM port assigned to the board may be too high. From zeveland:
"One little note if you aren't able to export and your USB board is trying to use a high COM port number: try changing the FTDI chip's COM port assignment to a lower one.
"I had a bunch of virtual COM ports set up for Bluetooth so the board was set to use COM17. The IDE wasn't able to find the board so I deleted the other virtual ports in Control Panel (on XP) and moved the FTDI's assignment down to COM2. Make sure to set Arduino to use the new port and good luck."
On the Mac, if you have an old version of the FTDI drivers, you may need to remove them and reinstall the latest version. See this forum thread for directions (thanks to gck).
What if I get a gnu.io.PortInUseException when uploading code or using the serial monitor (on the 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.java:72)
This probably means that the port is actually in use by another application. Please make sure that you're not running other programs that access serial or USB ports, like PDA sync application, bluetooth device managers, certain firewalls, etc. Also, note that some programs (e.g. Max/MSP) keep the serial port open even when not using it - you may to need to close any patches that use the serial port or quit the application entirely.
If you get this error with Arduino 0004 or earlier, or with Processing, you'll need to run the macosx_setup.command, and then restart your computer. Arduino 0004 includes a modified version of this script that all users need to run (even those who ran the one that came with Arduino 0003). You may also need to delete the contents of the /var/spool/uucp directory.