I thought we should have a thread about various tactics and strategies we use in the game.
1) Proton, Ion, Quantum:
The difference between them is... negligible. I vaguely remember that proton being weaker than others but not by much. Chose ONE and stick to it. Matter of taste really.
2)Missiles: slow and powerful. Useless against spies and units running away or moving away from you. Cannot be used as primary weapon for fleet but they are the best method to commit genocide. Nothing convinces people on planet to change sides like a barrage of nukes. at later stages extremely powerful.
3)Protecting your system:
A military base (proton, ion, or quantum) at jump gate + 2-3 squads of your best ships guarding it. nothing will escape it nor your ships will get destroyed. Perfect to max out experience level. This tactic is useful from episode3 and up. ep2... not so much.
4) Spies are THE most important units in a game. You should max out their level as soon as possible by using same ships all the time. At first they should be stealing money from your enemy. Great way to build up your planets at the beginning of your mission using enemy's cash. Then you follow up with invention theft. Finally when you are ready to begin invasion you should use spies to destroy military bases (one spy should get information on military in the system), planets defenses. Then before attack spies should start riots on the planet. The difference between using a spy or not is tremendous.
5)Heroes:
Assign them jobs as soon as possible. Later in the game I moved one spy, two governors and rest was soldiers. Having one more plot-related spy on my staff allowed me to send my two spy ships at the beginning of every mission to steal money without getting caught or fail. Governors increase your tax, moral and production output. Very important at the beginning.
6)Don't research what you don't need. Research points move to new mission so they do not get wasted if not used. At first you should research the techs which lower the required research point for everything else. Then I tend to research things which increase population limit on planet, income tax and moral (in this order).
having strong economy is more important than having newest guns.
7)Making cash fast:
Stealing should be your primary income. Mining bases are nice too. They do get depleted fast and it is pain in the buttocks to build them on planet with less than 200M people, though. I don't recommend increasing taxes. unless you have a very good governor on planet (who increases moral) and researched a tech which automatically gives a moral boost (without building anything). Interstellar merchant ships are nice too. it takes time for them to make the monies though.
8)Upgrading planets:
if a planet can house more than 1000M people without any modification, first thing you should build is factory, followed by population limit increasing buildings.
Unless it is your first planet in the mission:
Colonization ship followed by population ship and then housing project. You should colonize as many planet as possible as fast as possible. You can upgrade planets after they reach 500M
Above stuff refers to Singe Player Campaign from Legions of Iron.
Anyone wants to add something more?

Always start a mission by building up your economy. Tax income alone is typically horribly insufficient until you really build up your empire, and this is especially true in later missions where you start with a significant fleet (with high upkeep costs). Spies are great for generating income, as has already been mentioned. Trade ships are another great source of income once you control more than one planet (I personally prefer the interplanetary variety, since keeping them in-system tends to keep them safer). Two or three trade ships will take care of your money supply quite nicely. Mining platforms are often more trouble than they're worth, as they take a long time to move into position, and are soft targets that tend to get attacked quite often. Wreckage recyclers are typically not even worth considering.

A small dirty trick, force move a station into a wormhole and then deploys the sucker. That way when an enemy fleets pops into the system they get a nasty surprise, I am not saying it will defeat the assault, but it will definitly cut a big chunk out of them before it is dstroyed, esp. when the weapons are upgraded.
Be sure to built the station at a planet with atleast a military academy, a lvl 3 starbase will last a lot longer than a lvl 1.