As for the definition of terrorism, one typically attempts to pin it down as violence specifically targeted at the innocent bystanders. But that's not a very good definition, as any combat group fighting from an underdog position has to strike the enemy at where he is the weakest - even if it's the enemy's babies and cute puppies. People like Chakotay apparently tried to direct their strikes at "military" targets, to the point of ridiculousness (see "Dreadnought" where a planet-busting missile is aimed at things like fuel and munitions depots), while people like Eddington preferred soft targets like Cardassian colonies (as in "For the Uniform"). That's the difference between those who drive explosive-laden trucks at USMC barracks or explosive-laden boats at USN ships and those who fly aircraft at US civilian buildings - but that's not the difference between freedom fighter and terrorist.
Timo Saloniemi
Sorry, but I have to disagree here. As I see it, that's the difference between a freedom fighter and a terrorist.
A freedom fighter strikes against military targets and targets important for the enemies abilities to continue with the war and/or opression. He can also strike against targets which are of economic importance for the enemies.
Such attacks weakens the enemies military strength and his economical potential. It may also cause doubts among the enemies themselves about the possibilities to win the war or continue with the opression.
A terrorist strikes against everything, sometimes military and economic targets but most of all against civilian targets in order to create fear.
However, history has showed us that terrorism never achieve any victories. Look at WWII where the allied bombing of the German industires combined with attacks on the German army and air force led to victory while the terror bombing against civilians rather strengthened the German will to resistance and prolonged the war. Hitler's terror bombing against Great Britain didn't achieve anything either, it only strengthened the British resistance.
And look at ETA in Spain. They have slaughtered innocent civilians for decades now and what have they achieved? Nothing.
Not even the Basque population (which they claim that they want to liberate) want to have anything to do with them.
As for Star Trek, I can see a clear difference between the Maquis who fought for a just cause with mostly honorable methods and the Ansata (TNG "Higher Ground") who acted like terrorists and obviously didn't even know what they were fighting for anymore.