Apart from the one not connected to the outside world, each timer channel can be used to counte external events, generate a signal at a chosen frequency, or to trigger an internal interrupt after a given time interval or a given number of external events.
Somebody had an [adventure] with a race condition concerning the timer - disabling it in the same clock tick as it tries to trigger the external output can result in asynchronous behaviour!
The LPC21xx/PWM? outputs are based on a variation of the timer circuits.