Alien Ship Combat (Apocalypse)

Tactics in no particular order:

Buildings

• Spread your craft around the city close to the Dimension Gates (keep in mind that their location periodically changes). You don't need to have bases all over the city - send your craft to buildings which have multiple launch tubes. If you have your craft based at a building with multiple launch tubes, they will launch in such a way to use all available tubes - even if the yellow craft icon doesn't appear over an actual tube. Transtellar's Space Port is the best building with its 12+ tubes.
• After combat bring back your craft to base to refuel and rearm (if necessary) and afterwards send them to other buildings again. You'll only need to keep in your base the troop transports and any damaged vehicles.
• If your craft has sustained massive damage, try to land at the nearest building instead of trying to run back to base. Sometimes the best option, though, is a nearby and not the nearest building so that the enemy craft do not get a potshot at the landing vehicle, which are always easy targets.

Vehicles

• If you use Hoverbikes, then three stationed at the middle of each quadrant of the Cityscape works best.
• Hoverbikes are very weak. Use them as a swarm. 2 Hoverbikes agains 1 UFO only works in very early game. You'll need more later on.
• If you use hovercars, use them in pairs. Equip them with SD Turbo engines and 1 Bolter 4000 Laser Gun or Rendor Plasma GunRendor, 1 Janitor Missile Array or Prophet Missile Array and 1 Medium Weapons Control
• Hovercars can mount Small Disruption Shield later on. Remember this when considering to buy hoverbikes over hovercars.
• A mixed force of hovercars and hoverbikes are best. It can work well either way! If you want quick evasive bikes up close and personal with the hostile craft, then give them guns and give the hovercars missile weapons. You don't need to give shield to the cars, just weapon control modules. since then should be near a standoff range. If you want the opposite effect, give shields and guns to the hovercars for up close combat, and missiles to the bikes.
• One Valkyrie can easily be overwhelmed. Use more (6 Hoverbikes per quadrant, or 4 Hovercars, or 2 Valkyries) if you can afford it.
• Running low on powerful engines? Giving lower powered engines to missile launching craft can help the overall battle because these craft will be slower to get to an engagement (if you have to fly long distances across the cityscape quadrant). Hence, they will be able to lauch missles directly at the hostile craft instead of getting up close and personal and hoping that the missile can turn sharp enough to hit the hostiles. If you aren't lacking powerful engines, then this could be an option you'd may like to keep using.

Height/Aggression Level

• Using agressive combat controls can sometimes be worthwhile when up against a difficult enemy, because your ship(s) is concentrating on downing the enemy instead of trying to avoid its guns/missiles. It can get to the point where your ship rarely fires its armaments due to constant evasiveness. Be offensive not defensive.
• Changing combat attitudes of your attacking craft throughout the battle can help immensely. Fly to the alien craft using evasive control (don't waste missiles on hostile human cars), briefly switch to standard agressiveness so that everyone fires once (mainly for missile launching), change to full agression for craft with guns, change to cautious for craft with missiles. If a craft takes heavy damage, change to evasive control and disengage this craft. Don't forget to use the Pause button.
• Lower flying heights are important if you want to limit damage to the cityscape. When flying lower, you'll have to shoot upwards at the alien craft. If you miss, then the shots just go into space and not into a building. Another bonus is that you get "free" positive reputation with organizations if Aliens hit their buildings. It should be noted that large vehicles (Valkyrie Interceptor, Hawk Air Warrior, Retaliator and Annihilator) have slightly weaker top armor so they will sustain more damage when flying low once their shields are gone.
• A good tactic, although slightly uninspired, is to buy as many hoverbikes as possible and attack in swarms of 5-8 bikes per alien craft, set them on the second lowest height and set them to evasive. You should expect to lose one or two hoverbikes in each engagement in the early and middle stage battles. When fighting the larger alien craft it is better to barrage them with guided missles to soften them up before the hoverbikes get there, otherwise they will be dropping like flies.
• Also when employing the "Swarm" tactic, try to break up the groups of hoverbikes so they dont all get destroyed by a hail of missiles and cannon. Try to have 3-4 maximum coming from any one direction. It may be a bit of work but it pays dividends in the end.

Other

• This point cannot be stressed enough: make sure that you remove your agents from their vehicles/aircraft before sending them to engage Alien ships. If your craft is destroyed, the agent piloting it will perish too along with his/her equipment. Isn't that irritating?