The newer PIC's such as the PIC16F690 and the 28/40-pin PIC18FxxJ11 families have a Timer1 module with Gate Control which is ideal for doing this sort of thing.
6.6 Timer1 Gate

Timer1 gate source is software configurable to be the
T1G pin or the output of Comparator C2. This allows the
device to directly time external events using T1G or
analog events using Comparator C2. See the
CM2CON1 register (Register 8-3) for selecting the
Timer1 gate source. This feature can simplify the
software for a Delta-Sigma A/D converter and many
other applications.

Timer1 gate can be inverted using the T1GINV bit of
the T1CON register, whether it originates from the T1G
pin or Comparator C2 output. This configures Timer1 to
measure either the active-high or active-low time
between events.