Since the launch of Fermi, over 160 young, energetic pulsars have been regularly observed with 64 metre Parkes radio telescope, with the primary goal being to provide accurate ephemerides necessary to produce phase-resolved gamma-ray light curves. Here we summarize the current status and recent results of this pulsar timing program. In particular, we highlight timing analysis of PSR B1259-63, a pulsar with a Be star companion. We combine our observations of PSR B1259-63 with archival observations and show for the first time convincing evidence of spin-orbit coupling in this binary system. We also discuss efforts to correlate both glitch events and timing noise with changes in radio and gammaray emission.