These notes apply to the ​ATMega328P (Uno etc) using the Arduino IDE and libraries unless otherwise noted.

The 328 has 3 timers:

Timer0 (8 bits)

Default settings for Arduino Pro/Mini? (8 MHz):

TCCR0A: 3
TCCR0B: 3
TCNT0: 80
OCR0A: 0
OCR0B: 0
TIFR0: 0
TIMSK0: 1

Used for delay(), millis() and micros(). Don't mess with it.

Timer1 (16 bits)

Not normally used. For simple use, see the ​TimerOne library.

Timer2 (8 bits)

Used by e.g. the tone() function.