Base Defence Systems
Aliens will soon start finding -- and attacking -- your bases. At your disposal are a number of measures you can use to prevent these attacks from taking place.
Three fusion ball defenses with one grav shield is usually enough to prevent any UFO from landing, while six or seven FBD's with a grav shield pretty much make the prevention a sure thing.
Once aliens have found your base, they will continue to attack it until one of their craft make it past your defensive measures, and the crew are beaten inside the base. Once this happens, they will have to locate the base again before resuming attacks. The base defense screen is boring and gets repetitive quickly, so many players opt to not pay maintenance on defensive measures and simply allow the aliens to land. Given the advantages you have when fighting in your own base (where you have a very good idea of where the alien units will begin and what the layout is), and the fact that an alien commander is always present for you to capture, having aliens arrive could be considered more of a bonus than anything.
To minimize the chance of your bases being found, it is advisable to quickly shoot down any Scout ships on a Retaliation mission. You will need a Hyper-Wave Decoder to know what type of mission the ship is on. A Battleship may show up later, but if the Scout failed to find your base, the Battleship will not know where it is either. If the Battleship heads directly towards your base at top speed, you have been discovered, and you must fight.
An "optimal" base defense system might simply be a Mind Shield (to prevent aliens from attacking in the first place) and a well armed legion of soldiers (to kick them out when they do). HWP units are valuable for base defense (as they don't have to worry about psi attacks), but need to be accompanied by soldiers, or attacking aliens will destroy your base by default. Defending your bases is particularly easy if you have adopted a proper base layout strategy.
Make sure you sell off excess items from your bases' General Stores periodically, to avoid the 80-Item Limit bug. Many base-defense squads have found themselves armed with 80 Heavy Plasmas and not a single clip. Keeping ammo-free Laser Rifles and HWPs on hand can reduce this problem, as they are at the top of the inventory list and are distributed first.