First things first.. If he's bombing a planet, get the ships doing that first. Siege frigates and cap ships are the only thing that can bomb your planets. Get those and it's safe. Or if it's going to be a while ( single cap ship ) chase the other ships. It depends on what they are bombing. Asteroids with no upgrades ? Let them bomb, I'll be busy killing expensive ships.. Planet with full upgrades ? Save that sucker first.

You're either thinking about pirate raids, or your enemy is using the 'by-pass' ( essentially jumping through your edge planets and attacking your core ). There are various theories on how to handle this.
1.) Jump Inhibitors on your edge planets work well, they keep them from jumping out.
2.) A reserve fleet is another good option. It helps defend the edge planets, but can jump back to defend or forward to attack. This is the best option.
3.) You can re-inforce with static defenses. Static defenses are the least useful against a human, since they can be picked off. BUT, they are the MOST useful against pirates because they never seem to attack the actual defenses. Some prefer turrets, some fighter bays. I use 5 fighter bays with the rest in turrets ( I max defenses at every planet ).

For pirate defense, personally I just use static defenses. For humans, I use everything.

Anyone have any counter to the Novalith prototype? What if a player drills down this track fast, half way through the game they have five cannons blasting planets off the map. How can you fight this in a single star map? In my last game, my game partner (thankful for me) had 8 Novalith cannons. No one stood a chance. His edge fleet was decent enough to hold off the invading forces.

The best strategy against noviliths is a very aggessive one. Its simple...keep the pressure on them enough and dont let them build them. If your oponent builds several novaliths your fleet should be at an advantage (he spent alot of resources and research time to get them). Simply hit'em hard, hit'em often

Fighters are way better vs Siege frigates than Bombers I believe.

I've used all fighters for a few games. They're fairly effective. I'm not to worried about caps bombing my planets (unless it's a Marza) when the AI has 5-6 bombers going at it. Recently I've been doing 1 bomber/1 fighter per hanger with mixed results. I'm going to switch it to 2 hangers 3 fighters 1 bomber.

Vs. AI you find an awful lot of frigs and carriers making fighters more ideal in many situations.

To bad there isn't a flak turrent...

Are there any unofficial maps?

I placed them in the right folder, but as soon as the game starts, it says that everyone is defeated and the space is blank.