Lvl 1 Gaia: Total bonuses: +20% capacity, +20% mining, +20% credits, -30% combat
Lvl 2 Gaia: Total bonuses: +40% capacity, +40% mining, +40% credits, -60% combat
Lvl 2 Gaia +2 x 10% structures, +15% planetary combat commander: Total bonuses: +40% capacity, +40% mining, +40% credits, -25% combat
Yeah bonuses stack, the stacked value is what you see in the planet interface as Total bonuses. There are no other hidden bonuses (except colonists absorb

), all bonuses are displayed in Total Bonuses.
Some planets have rough terrain that gives them an edge in combat, starting with the toughest terrain and ending with the Gaia paradise that actually has a combat penalty. Wealth, high economy and sitting at the beach tends to make your colonists lazy in combat

Each planet type has it's own bonuses that you can see in the planet guide:
http://wiki.spaceo.net/index.php/Guide:Galaxy:PlanetsHere is a pic (Gaia with 15 x 10% combat structure and some commander ability):
http://www.spaceo.net/scr/planet_gaia.jpg