My favorite, especially when playing against Starfleet Commander AI's, is to use Heavy Beam Cannons and Grav Turrets in early game. Granted, there's a limit to how many HBC's you can have, so with multiple planets you'll need more than those. Grav Turrets are nice against Raid Starships though. Slows 'em down considerably, and if coupled with HBC's, you get lots of firepower focused on them. This way you can keep most of your fleet elsewhere and trust in your defenses being able to handle a few errand starships.