Alien bases are always in the same place, but appear at different times. If you know where one usually is, fly an empty Skyranger into the area and sometimes the purple square will come up. At this point, get a strike team together, because the aliens will get many points from having a base on earth.
I can only remember where a couple are and that is - Madagaskar (Island to the east of the African mainland) and one very close to the Russian border, about 800 km east of it and on the north tip.
Another tactic is to let the base stay and shoot down the Supply Ships carefully with an interceptor with 2 plasma cannons (damageless to the interceptor and no elerium needed to power it - works on Terror Ships too) and then kill off all of the aliens for a lot of Elerium + Alloys + Corpses and Weapons.
I personally do that a couple of times so that I get loads of Elerium, and then just attack the base before it starts sending out Terror Ships etc.
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