Federation (Manheim Effect): Averted, so long as you can master using it. It can time-freeze enemy units anywhere on the map, and while it takes a long time to charge up, it can be used to devastating effect by taking out the enemy base's first line of defences.
Klingons (Subspace Shockwave): Averted; probably the most genuinely useful of the superweapons, as it has a fairly long range and can be unleashed to devastating effect on enemy bases.
Romulans (Subspace Rift): Definitely the case, as the craft that carries it has to be placed right in the middle of whatever enemy formation/base you want to destroy, and its shields are barely stronger than a scout ship, meaning that it's likely to get blown away before it can activate.
Borg (Transwarp Gate): Not so much in the first game, as it's an easy way of dropping your ships into an enemy base (just don't leave the gate open too long, or the enemy forces can fly back through it into your own base). Definitely impractical in the second however, as warp drive nullifies its main advantage, and it's a waste of money compared to the fusion cubes.
Cardassians (Dreadnought): The same basic effect as the Subspace Rift, but it comes in a missile that has to be crashed into whatever you want to destroy. It's at least a bit faster than the comparable Romulan ship, but that doesn't really affect the enemy's ability to target it, and it has even weaker shields.
Species 8472 (Combination Beam): This involves getting between 3 and 8 ships to slave their beam weapons together to form one huge blast. In theory this should be a good way of taking out things like starbases and fusion cubes, but in reality it's probably the most blatant example of this trope in the series. The range is too short, the charging time is too long, and the AI's targeting priority system means that the formation will always be attacked whenever it gets near the intended target, and likely wiped out before it can fire the combined beam.
Game Mod: The first game was known for being exceptionally easy to create mods for, which led to a huge modding community springing up. Unfortunately the developers either didn't get the memo on this or actively disapproved of it, and so the second game was designed in such a way that most weapon functions couldn't be modified, and any significant amount of modding could actually break the game installation altogether. Some modders managed to work their way around the game's restrictions, but the Armada II modding scene never took off in the way it did with the first game
Geo Effects: Provided by nebulae, and lots of asteroid belts. Black holes slow ships down, and will suck them in if their engines are off-line. Yellow Mutara Nebulae slowly kill off crewmen, and green nebulae somehow cause your ships to get repaired faster.
Glass Cannon: In the first game, the Federation and the Romulans have a class of ship that fires tricobalt torpedoes, which a long-range, very powerful Do T weapons. The ships that fire them have got the shields of a scoutship, so don't send them anywhere without an escort.
Green Rocks: Dilithium, which everyone needs to power their ships and build new ones (except species 8472).
Hey, It's That Voice!: Patrick Stewart, Michael Dorn, and Denise Crosby reprise their roles as Picard/Locutus, Worf, and Sela.
The captain of an Aegian class was voice-played by Jonathan Del Arco, Who played Miguel Diaz.
Del Arco also played the Borg drone Hugh aka Third of Five in the TNG episodes "I, Borg" and "Descent II".
A Millionis A Statistic: Inevitable, with how the games model crew complements for ships and stations. You need to build Starbases and colonize planets to replace you're losses, but then again, it's the most plentiful resource in both games.
No Canon for the Wicked: The Borg campaign ends with Worf and Deming dead, and Earth assimilated, but it's eventually undone by the Enterprise travelling through time to avert it.
Obvious Beta: The first game suffered a really bad case of this on its initial release, and the 1.1 patch didn't do a whole lot to help things. Worse still, Activision cut off support for the game only a couple of months after its initial release, leaving incoming Armada II developers Mad Doc Software to create a 1.2 patch that finally fixed all the major problems with the game. Armada II itself suffered a few bugs on its initial release, including one very obvious problem in that ship explosions weren't implemented properly, but was nowhere near as bad as the first game.
Ominous Message from the Future: In the first game, the USS Premonition comes back in time to warn the Enterprise of an imminent Borg attack that will eventually lead to the entire Alpha Quadrant being assimilated.
Organic Technology: Species 8472 are all about this, they even Transmute all other resources (including people) into Bio-Matter, before they can build with it. Because of the Organic Technology they are also a bit different to play, growing their ships from larvae, only needing one crew member per ship and have a weaker, but mobile, star base.
Pursued Protagonist: Captain Denning and the USS Premonition in Armada 1. And later the USS Avenger with Worf in command.
Shout-Out: One of the Borg's standard responses, "By your command," is a standard Cylon response in the classic Battlestar Galactica.
Standard Sci-Fi Fleet: The developers took artistic license to a bizarre degree on a few of the ships. By far the most egregious case is with the Defiant Class. In DS9, and in Starfleet Command 3, the Defiant is a small overpowered warship capable of taking down ships five times it's size singlehandedly. In the Armada games, however, it's more or less Cannon Fodder and doesn't stand a chance against anything larger unless it's part of a fleet. And even then...
The first game was a LITTLE better about it, presumably because of the smaller ship pool (and because Worf uses a Defiant as his ship). However, in the second game, you're likely only building the basic shipyard because it's a requirement to build the advanced shipyard and gain access to the more powerful ships in your fleet.
Subsystem Damage: Various parts of the ship can become assimilated or damaged, and many special abilities (and nebulae) temporarily disable certain ones. Repair times are influenced by how many crew are aboard, so replace you're Red Shirts often!
Timey-Wimey Ball: Where to begin? The Premonition is from a future where the Borg have assimilated the Alpha Quadrant, but it continues to exist even after history has been altered to the point where it should never have been built. The Enterprise is sent back in time just before the Borg win the Battle of Earth and proceed to assimilate the planet. In a "new" timeline, the Enterprise returns to Earth with a massive fleet of reinforcements just in time to stem the tide... then orders the Enterprise already there to go back and takes its place, which should result in two Enterprises, not one. A Borg cube goes back in time just at the moment of Locutus' defeat, destroys the Enterprise-D just after Farpoint Station, forcing the Premonition to go back and avert that event and protect the future. Yet, Picard remembers this event at the very start of the game! Finally, at the end of the game the Premonition quietly returns to the future... a future concurrent with the timeline they're in, meaning one where the Premonition was never built — and versions of Denning and the crew already exist.
Well... Both games include a Borg mission revolving around Assimilation. Species 8472's resource harvesters can literally suck people straight from their ships or colonies, to be turned into Bio-Matter!
Red Shirt Army: Every race (except Species 8472) has these (or Mooks, depending on the race and circumstances). Note, that whenever you try taking over an enemy ship or station, more than 5 reds shirts die every second that they're fighting the defenders and/or fixing life support.
Zerg Rush: More or less the only way a Venture or Defiant can take down large opponents in these games.
This is literally the only way to capture enemy ships or stations, see Red Shirt Army above.
Zombie Apocalypse: Averting this is the reason the Premonition exists, and the entire point of both games. Also, don't let the Borg near your colonized worlds in Armada 2, aboard your ships in either game...