Atrocities? It depends. I don't obliterate bases, mainly because the happiness isn't the same system as Civ 4. Planet Busters are rare for me. I don't typically deploy nerve gas, mainly because I can use the slot for something else, or just cheaper build price.
When I'm in a brutal mood, or I just want to annihilate the other faction that keeps blocking my attempts to become Supreme Leader... Then I execute Operation Miasma
Step 1: Preparation. Build swarms of Clean X Choppers and Needlejets. (Clean is necessary because I'll be building lots and starting several dozen turns before I begin.) If they have Secret Projects that I want, I'll add Drop troops.
Step 2:Targeting. Build seabases just next to their coast making sure that most of their bases are in Needlejet range, along with lightly threatening bases next to other factions incase of pacts.
Step 3: (Optional) Diplomacy. Repeal the Charter. If not possible, then prepare for economic hardships due to embargos.
Step 4: Engagement. The core of this doctrine holds that the military is not the target. Civilians are. Each attack with nerve gas wipes out a pop or two. This can quickly destroy any base. You only capture if you need a new launch site for your choppers, or they have Secret Projects, so you attack with drop troops.
Step 5: ????. Remember what were you doing this for.
Step 6: Profit!. Enjoy the spoils of your war as the Supreme Leader of Planet! Use this strategy to dominate the other factions! Stop their attempt at Transcendence! Save the Planetary Energy Market! Sure, you're the most brutal warlord in human history, and future historians will say that you were worse than Stalin and Hitler, but there will be peace in your time!