One of the oddest things to me about GC is how you have to genocide a planet to conquer it.
When it comes time to invade it's a good idea to have a strong economy and a little buffer of BC in anticipation of the financial hit of conquering worlds.
I generally get rid of structures I won't need when I take a world.
If the population after invasion is drastically low, I'll sometimes dump a transort full on it and send the transport back to an established (research) world to refill.
I usually have my production and research rolling by the time I'm invading, so newly conquered worlds will generally be specialized for BC generation unless they have significant bonus tiles or a huge investiment in structures I'd eventually want.
Another thing I like to try to do when it's time to invade is have a few constructors ready to pounce on any resources I can liberate. If the race you're invading has any econ or morale resources, these can be a big help to the econ hit from invading.
One suggestion I would make (even though it wasnt your question!) is your approach to the invasion of an enemy. Instead of the somewhat gradual way of taking out their starbases, freighters, and waiting to get PI rsearched, instead wait to declare war until you have the transports ready to go. Target the planets as your initial actions of the war, and they wont get any time to respond to your attack. Hit them hard & fast. You can always mop up the bases and other random things after you've already taken a number of their worlds.
I agree with this too. I generally don't go to war with the AIs just to terrorize them (if they start it then I might do it, while ramping up for invasions). I initiate wars to conquer planets and resources. I like to have transports ready to go and I like to take out (ideally multiple) objectives quickly. This makes it harder for them to react/rally and minimizes the chances of external factors (random events, other races) mucking things up.