There are two important reasons for a series resistor:
1) in circuits with a dual supply op amp driving the varactor, you can get a situation (during start up, etc) where the varactor diode becomes forward biased. If there is no current limiting resistor, then the varactor diode can actualy blow up.
2) A typical PLL has a "lowpass response" rolling off starting around 10KHz to 100 KHz. If you have a reference fequency of maybe 2 MHz, then that 2 MHz spike noise is not going to be very well attenuated by the standard loop filter. A common improvement to the loop filter is an R-C lowpass filter that will knock that reference spur down another 20 dB or so. To add one, though, you have to make sure the additional R-C phase shift at the loop bandwidth edge is not so big as to cause control loop instability.
Rich