Lots of bonuses available. The red military resources are the best and you can have more than one. You also get bonuses from the tech tree.
As mentioned above, with Thalan's and the right techs you can get to +60 on a resource node and +36 on an economy base. These are all percentages.
You also get 1 or 2% from anomalies. They add up alot during a long game. (with lots of surveyors)
Check you Civilation Stats for your bonuses. You can get an AI opponent's stats from espionage.
These are percent bonuses. So a ship with 30 missile and 30 armor might end up being 90 missile and 90 armor with a 200% weapons/defense bonus. You can make some very powerful low tech ships this way. Lots of fun for number crunchers like me.