Phase jump inhibitors are a big thing in this situation.  If you are vasari, you could have an egg with grav warhead.  If you are advent you could use repulse.  You could throw a small contigent of ships in front of it to slow them down(scouts work well for this because they are fast and cheap).  You could split your forces and be waiting for them in the next jump.  Phase inhibitors are best though.

[_]-Greyfox

On multiplayer this is usually used as a stall tactic.  Sometimes it will be because you have a large fleet but a smaller econ, other times the person is hoping to get reinforcements from an ally, and other times he is just trying to get under your skin.  I recommend doing 2 things...

1. Only chase him with enough ships to deal with the threat.  Don't send 50 ships chasing 15.  If half your fleet can deal with his running fleet, send the rest on the offensive and make him pay for having his ships so far from his planets. 

2.  Phase Jump Inhibitors/Repair bay combo.  Try to trap him with multiple jumps through phase inhibitor protected gravity well.