* BlackAndGreyMorality: Throughout both games, the Shivans are treated like the villains, attacking and destroying randomly and without warning, yet from Bosch's description, and from the Ancients' monologue, it's possible that at least in the case of the Ancients, the Shivans were only preventing the Ancients from causing more destruction. And while it isn't guaranteed, it's possible that if the Shivans hadn't showed up, or if the Terrans and Vasudans had never made contact, they may have followed the same route, and vice versa.
* DemonicSpiders: SF ''Dragon'' fighters are tiny, absurdly manoeuvrable, and damnably well armed and shielded, rendering them ridiculously hard to catch and destroy if they don't get into a close-ranged dogfight; and even then, they're damned near impossible to hit, as they can literally fly circles around any ship in either game. Their only weakness is that their armor is made of tin, but putting on primary weapons that are good against shields turns most other fighters (which focus on hull strength instead of shield strength) into DemonicSpiders of their own. The developers damned well knew it, too, because in one mission two full wings of ''Dragon'' fighters pop up at long range just to scare you [[spoiler: before the detonation of the Meson Bomb annihilates them]].
** In either game, if you are already very good at swatting ''Dragon'' and ''Manticore'' fighters, then this title belongs to the ''Nephilim'' or ''Seraphim'' bombers; most of the time, these are the very things responsible for Mission Failed. They are slow and big, but are so ridiculously armored and shielded they can shrug off up to three hits from Trebuchet heavy missiles. In addition, the ''Nephilim'' has seven guns linked to one gun slot, giving it [[MoreDakka a ridiculous rate of fire]]. The ''Seraphim'' has more guns, but in 3 slots. Both bombers have a pair of turrets that can fire at you even when you are not in front of them.
** If you're defending capital ships in the second game, you will learn to loathe ''Lilith''-class cruisers. Their main beam cannon is extremely strong for a ship of that size, and their small size means that other capital ships will have a hard time hitting it when shooting back. They also look near-identical to the ''Cain''-class, which is a total pushover and easy to kill.
* EnsembleDarkhorse: Lieutenant-Commander Snipes. Probably due to being the only named pilot in the story, and getting the best lines in the game.
* EvenBetterSequel: The original game received reviews that, while mostly positive, were nothing particularly outstanding; it was considered a good game, but not a ''great'' one. ''[=FreeSpace=] 2'', on the other hand, was positively heaped with praise, received numerous 'Game of The Year' awards, and is still widely played even to this day, over a decade after its release.
** Due to the fact that ''[=FreeSpace=] 2'' was one of the last games of its kind ever released, some fans jokingly claim that it was so good it killed the entire genre, since nothing else would ever be able to compete with it. (The real reasons the Space Sim genre died out are a lot more complex.)
* FanonDiscontinuity: "Silent Threat". The original has now been supplanted by a (''extremely'' well-done) fan-made revision of the entire thing called ''VideoGame/SilentThreatReborn'', which keeps the storyline largely intact while adding enough to it to make it good, and has pretty much been unanimously declared to be superior to the original product, thus pulling the story out of FanonDiscontinuity.
* GoddamnedBats: Manticores and Amuns are annoying too.
* GoodBadBugs: In ''Argonautica,'' you have to defend GTD Aquitaine while it waits for a transport delivering materials to repair its disabled engines so it can jump out. If you fail to defend the transport itself, Command will send a panicked message about the transport being destroyed...and a few minutes later, the Aquitaine's engines will magically repair themselves anyway.
* MagnificentBastard: Admiral Bosch. While his ultimate fate is [[WhatHappenedToTheMouse ambiguous]], he fools Alliance at their every single attempt to take him down.
** To be fair, it is heavily implied that the Alliance let Bosch succeed for as long as he did because they knew about and wanted him to complete the ETAK project, so they could steal it for themselves. This meant that the GTVA likely could have stopped Bosch and his killing of countless Vasudans earlier, but kept the war going so Bosch could finish the project. Had they stopped him as soon as they could have, it is unlikely they could have finished the project, given that it was a cancelled attempt at creating a communication device to contact the Shivans (which appears very hard to do) and that Bosch took extraordinary measures to destroy the project's notes.
* MemeticBadass: Due to the friendly AI's general incompetence and the ridiculously high number of kills you score throughout the game, the player's character, only ever referred to as "Alpha 1", has become this.
* OnlyTheAuthorCanSaveThemNow: Towards the end of the second game when the Shivans start to take the war seriously. It ends in a Deus Ex Machina that was probably meant to be explained in the third game ([[spoiler: the Shivans blow up Capella's star as the humans retreat and then most of them warp out to an unknown destination.]]). To be fair, the GTVA was about to seal the last remaining jump node out of the Capella system leading to GTVA territory, with pretty much the exact same method and means you'd just successfully used the mission before (which was based on the finale mission of the first game, too). Still, everyone knows it's just a temporary measure to buy time, time that can be used to get stronger, more prepared, and more advanced. Given how far the GTVA advanced in the 32 years between the first and second games (especially after having to recover from the loss of Vasuda Prime and loss of all contact with Earth, and far more destroyed colonies), it's not unreasonable for the GTVA to be capable of standing against the Shivans in another several decades. Not outmatch them, but capable of actually holding their own this time.
* ThatOneLevel: "A Game of TAG" from Freespace 2. Your loadout is preset to a Ulysses fighter (which even the briefing admits is a Great War antique), a Prometheus-R Cannon (which is basically useless) and a Sublach HL-7. Your also given the TAG-A - a weapon that allows the nearby corvette to direct any weapons in range to destroy even fighter class vessels. All this sounds cool until you realize that the TAG-A is a dumbfire weapon, meaning that it has no guidance systems whatsoever: if the target moves, you miss. You also have only one wingman, with the same armament. Making things harder are the matter of the Taurvii-class bombers the level likes to throw at you, which are both fast and have a thin target profile. And to top off all the frustration, the level is set inside a nebula, meaning even the most accurate pilots are going to struggle to land shots, and the corvette accompanying you cannot defend itself because ALL of its guns are linked to your TAG Missiles (so in order to make it defend itself, you need to TAG a Shivan craft). For maximum funsies, after forcing you into an obsolete and undergunned fighter with little backup, Command will guilt-trip you about needing to defend the corvette and AWACS ships while sending you no reinforcements. Expect to fail many, MANY times, even on re-runs of the game.
* WhatAnIdiot: See that page for the details, it's lengthy.