the drive you boot to i usually the master. the slave is considered a secondary drive; either for user data or another os.
cable select - http://en.wikipedia.org/wiki/Cable_select
Cable select is a setting on IDE devices such as hard drives and CDROM that allows the position of the drive on the cable to select whether the drive will act as master or slave. This setting is usually performed by placing a jumper on the cable select setting, usually marked CS. Pin 28 on an IDE cable is used to decide the fate of the device. If the signal of the device is grounded, then it becomes a master, if ungrounded, it becomes a slave.
Cable select is often used when people are frequently switching around drives (e.g. when performing hardware maintenance). There are two main disadvantages to cable select. Most older 40-pin IDE cables do not support cable select and need a special modification to enable it, but newer 80-pin cables support it. Also when moving drives around the BIOS and operating system may get mixed up and attempt to boot from the wrong drive. Due to these disadvantages, many people prefer to explicitly setup their masters and slaves by manually moving their jumpers.