Over the several games I've played, I find that my troop transports zip by undefended star bases and troop transports. However, I can never blow them up. So, I started arming my troop transports with the most basic weapon possible (this is especially easy late game or with a robust economy/tech). When transports are running around with 15+ movement, I can zip in, kill 5000 undefended troops, and zip out, and very rarely do I have to divert my combat vessels (who move slower due to lots of weaponry) to chase the transports down. It's no Einstein strategy, and I'm not Wyndstar, but it's a little something I do that's cheap, easy and pays big dividends.