Good space RTS with customizable ships?

Pax Imperia: Eminent Domain

Maybe Gratuitous Space Battles

Sins of a Solar Empire: Rebellion ?

Nexus: The Jupiter Incident?

The best and most customizable space 4x is Aurora ( pentarch ), nicknamed the dwarf fortress of space.
That is unless you prefer graphics to deepness.

http://www.bay12forums.com/smf/index.php?topic=47678.0

You have to design the equation between how big your missiles are, how fast, how agile, how powerful, and they need their own adapted launchers and targeting systems. And obviously they will need to rearm, meaming that it also implies thinking about logistics instead of just sending a thousand ships with infinite ammo into the unknown ( where they would die anyway due to various failures and lack of fuel ). And those cool shield eat power, and those bigger generators make bigger targets... Designing a spaceship and its equipment basically requires a degree in engineering. Or close enough to scare the noobs and ravish people who want a real spaceship game and not just some pretty 3D explosions.

Battlecruiser 3000AD also has a lot of customization that isn't found in modern games.

Although more a Space RPG RTS hybrid, Starsector - formerly known as Starfarer - is a formidable game where you have a large control over your ships, both their weapons and hull mods.