High resolution timer on the BeagleBone?
Yes, DMTIMER - see page 3729 of the Sitara Arm Cortex A8 Technical Reference Manual.  It can accept a wide range of clock frequencies and has a programmable prescaler allowing values from 1 to 256.  For example, it has a precision of 37ns when fed a 27MHz clock with a prescaler of 1 (Table 20-1 in the manual).  However, if you're using an operating system chance are it's already utilizing that timer and you'll be dependent on the operating system for timing.