Quite possibly the best program for computer clock synchronization is NTPD. Far from just changing your computer's clock to agree with some other time source, NTPD offers a wide array of services. NTPD can compare your computer's clock against an external reference time source over a long period of time. It can then measure the 'drift' of your clock and apply a correction. This will keep your clock more accurate even if the external synchronization is later removed. It will also reduce the need to 'jump' your clock to keep it in synch. NTPD can allow a computer with a more accurate time source to provide time to other computers. More than 100,000 computers currently form a network of time servers and clients on the Internet.
This network can have many levels. For example, a computer with a GPS clock can provide synchronization for several servers which in turn provide synchronization to thousands of client computers. NTPD can compare time accuracy and stability from numerous sources and pick the best one to lock your computer's clock onto. If your GPS clock suddenly goes haywire, NTPD is smart enough to know not to listen to it.
NTPD can filter multiple time readings to reduce the effects of jitter. A single time reading may be off due to network congestion or server load. NTPD is smart enough to pick the best readings and use them.NTPD also monitors its own accuracy and the reliability of all the time sources it is using. This statistical information is invaluable in determining of your clocks are actually synchronized. It will also tell you if a change you have made has actually made things better or worse.NTPD works for almost every version of UNIX that there is, including Linux and FreeBSD. Unfortunately, accurate clock synchronization is not possible on Windows 95 or 98 -- you can only synchronize them to about a half a second and only by a series of clock jumps.
Almost all GPS receiver modules provide a serial output of some kind. The protocol supported by most GPS receivers is called NMEA-0183. This is a standard for communication between marine devices developed by the National Marine Electronics Association. Unfortunately, none of the standard NMEA-0183 messages contains a precise time code. The best you can do without using any proprietary extensions is to configure your receiver to send an 'RMC' message every second. An 'RMC' includes the date and time down to the second.