Car Fu: Get strong enough, and you can heft cars. Get to the maximum level of strength, and you can toss them all the way down the city block. And given that they don't cost Prestige points at the end of a level, one smart strategy is to gather as many damaged(so they stop moving) cars as you can, then find a way to lure the major bosses of the stage into a 3 car pile-up. Which you detonate by throwing a fourth car into them...
Dangerously Genre Savvy: Blitzkrieg, the Big Bad of Third Reich. To protect his base, he uses the "barrier" method used by Nuclear Winter in the beginning of the game but removing the weakness that allowed the heroes to cross it (making it go underground, so that the Ant can't burrow underneath it. When the protagonists manage to enter the base (by travelling further back in time to set a bomb in the barrier generator), instead of facing them directly, Blitzkrieg instead creates portals to the future from which he summons endless waves of mooks to overpower them. Only when Alchemiss manages to reverse time and order the protagonists to destroy the machines that create the portals (which were previously invisible) and thus is left with no other options does Blitzkrieg engage the team directly.
Don't forget, when the team goes back in time to plant the bomb in the barrier generator, he doubles the amount of guards in past, which means the guards in present get doubled too. He also launches several new weapons.
Demoted to Extra: Minuteman is more or less unnecessary after the first couple missions of the second game. Mentor and Alchemiss are the real main characters, along with the WWII-era heroes.
Dating Catwoman: Minuteman and Red Oktober get rather friendly in the second game.
Destructive Savior: Freedom Force are indisputably good guys, but they tend to cause a lot of damage to the cities they're defending; aside from the many tactical applications of environmental destruction, they'll likely level many buildings entirely by accident over the course of the game.
Can be annoying when the objectives are "Don't let X building be destroyed", meaning you can't use things like Disruption or Ignition.
Die, Chair! Die!: Pretty much every item of scenery, from small rocks, to chairs and fences, to cars and boulders, can be thrown for damage. It is possible to completely curbstomp otherwise-difficult bosses by launching cars at them from halfway across a level with your super-strong heroes.
Dirty Cop: A few missions feature "Crooked Cops" as enemy mooks.
Pure Energy: Man-Bot and a number supernatural or laser weapon weilding enemies.
I Love Nuclear Power: Microwave. And Nuclear Winter's melee attacks. Mentor can learn a radiation beam power late in the game. Also, expect most kinds of laser weapons to do radiation damage.
Functional Magic: Alchemiss, Quetzalcoatl and Red October and her minions. It's used mainly for debuffs, while Quetzacoatl can also buff and heal allies with it. Offensive magical powers do energy damage.
Psychic Powers: Mentor and Blitzkrieg. Only used for status effects though.
Casting a Shadow: Shadow and her minions, of course. But it is only a stealth power.
Enemy Mine: After you kick him around a little, Lord Dominion opts to teleport Freedom Force to Time Master's domain so they can stop him from destroying all of creation. In vs. the Third Reich, Freedom Force digs up Time Master himself so he can fight Entropy. You also get control of Red Oktober for a level.
Exactly What It Says on the Tin: Freedom Force vs. The Third Reich. Subverted in that only about a third of the game involves the Third Reich, with Nuclear Winter and Entropy getting almost equal billing.
Expressive Mask: There's some of this to be seen in Freedom Force vs the Third Reich. It's most visible with Black Jack and Alchemiss. Tombstone even gets Oddly Visible Eyebrows for a scene or two.
Mentor has shades of both Professor X and The Martian Manhunter.
El Diablo is a Spanish (Latino-American with Mexican roots, to be percisely) Human Torch.
For another Man-Bot is essentially a combination of Dr. Strange (his original rich playboy lifestyle/humbling origin), Cyclops (his energy powers and inability to control them), and Iron Man (his armor itself)
Most of all comic heroes, he resembles DC's Human Bomb.
Alchemiss is the Scarlet Witch with the story arc of Jean Grey in the sequel.
The Ant is pretty much Spider-Man, for instance, with ant-related powers like burrowing and super-strength and gadgets that shoot acid. The ant motif may be slightly inspired by Ant-Man, as well.
Bullet is any number of super-speedsters including The Flash and Quicksilver.
Man O'War is Aquaman if he was played by Sean Connery, with the flight and electric powers of the Silver Age Sub-Mariner.
Sea Urchin resembles Jubilee, being the Bratty Half-PintSidekick of the rather gruff and edgy Man O'War. Oh, and her power is making acidic bubbles.
Game-Breaking Bug: There are several bugs that were never patched for the first game, even when it was made available on Steam. Certain computers experience issues with collision detection and saving. Because Technology Marches On, a new issue crops up when the game is played on newer versions of Windows when exiting out of the game: Windows will state that the game "quit unexpectedly" (despite it actually being stopped manually by the user) and "stopped working". Several other issues, such as map boundary issues and graphics glitches, can only be fixed by using the esoteric "Compatibility Mode" option in Windows 7.
Game Mod: So, so much. There were quite a few websites devoted to making downloadable game content, including character models for a vast amount of classic superheroes, as well as full mods that added their own storylines and missions. Some of the more famous ones included the DC Comics mod, which told an original Crisis Crossover story set in the DC Universe. There was also The Great Hunt, another Crisis Crossover which included DC and Marvel characters, as well as pulp and obscure ones.
Annoyingly, some people can't get the Steam versions to run mods for a reason the fandom has yet to discover.
Heroic Willpower: All heroes have one Hero Point, which can be spent at any time to trigger a burst of Heroic Willpower that will instantly fully heal the hero, restore all their energy, or allow them to shake off any status effect. Minuteman can get extras, which helps to offset his squishiness.
The Grim resolve ability makes characters immune to knock-back through sheer force of will.
Heart Is an Awesome Power: The Ant has a Shove attack, which can knock an enemy back but does no damage. Increasing the power of a shove just knocks back an enemy farther. What purpose does this serve, you ask? Well, see, on some maps, there are bottomless pits... You can also hurt folks by shoving them off buildings. Alchemiss had a similar power, which didn't require you to get up close to the enemy.
Informed Ability: The Domain, under Lord Dominion, reportedly has access to a vast battlefleet that can and has conquered entire dimensions, leaving Earth as the only free world left in existence. Do they ever demonstrate anything that suggests that scale of military might? Not really, no.
Instant Fan Club: Somehow, Nuclear Winter is able to get a small army of Soviets with Ice Rays within a few hours of his transformation from a more-or-less normal guy into a full-blown supervillain. Everyone else has some explanation for where their mooks come from.
Well Sukhov was already a presumably high ranking Russian secret agent so it makes sense for him to have a bunch of flunkies at his command. As for their ice based weaponry, it was probably supplied by Lord Dominion or Timemaster.
In the Hood: Shadow in the first game, Red Oktober in the second.
Jack of All Stats: Minuteman. His attack is high, but not as high as Supercollider. He's fast, but not as fast as Bullet. He's tougher than many team members but cannot compare to Microwave or Man-bot. He cannot fly, but he can jump over buildings. An overall decent character, but not exceptional in any particular area.
Love Makes You Evil: Entropy's plan is simple: compel Man-Bot to stay with her forever by holding all of reality hostage. Either she gets her man, or the universe crumbles until Entropy and her man are the only things left. Either way, they'll be together forever.
Mad Artist: Mr. Mechanical. Despite the name, he's actually an architect... with a somewhat destructive sense of aesthetics.
Made of Iron: Literally. "Metal" is one substance a character can be made of, which renders them near Immune to Bullets and blunt force, but vulnerable to Energy X attacks and electricity. This includes the very human Sky King, due to his metal armour.
Nice Job Breaking It, Hero: The Freedom Force doesn't know it, initially, but part of the purpose of the Domain is to contain Time Master. When Freedom Force opposes Lord Dominion's plans, they advance Time Master's schemes... and Time Master is much, much worse than an alien dictator.
Personality Powers: True to the '60's Cliché Storm, most characters have Energy X abilities that are related to their personality in some way. Minuteman was a patriot before he was a superhero, El Diablo was always Hot-Blooded, and so forth.
Phlebotinum Rebel: Lord Dominion's master plan is to amuse himself by giving superpowers to the scum of society so he can sit back and watch Earth tear itself to pieces. Mentor interferes, causing Energy X to be spread at random over Patriot City and creating the superheroes.
Pyrrhic Victory: Timemaster is defeated, but at the cost of stranding Man-Bot in the celestial Clock, forcing him to face the Wraiths of Chaos for all eternity. Poor guy, 'cause when Alchemiss rescues him the entire universe is put in peril and he loses Alchemiss permanently. He just can't catch a break.
Pyrrhic Villainy: Time Master's plan is to destroy the multiverse in order to gain immortality. Wouldn't he get bored after a while with nothing but himself in existence?
This gets pointed out/lampshaded by Man-Bot. Apparently Timemaster doesn't mind.
Sealed Evil in a Duel: At the end of the first game, Man-Bot stays behind in the Celestial Clock to allow the rest of Freedom Force to escape back and is trapped there forever. His presence there causes creatures of chaos to attack the clock, and he has to spend the rest of eternity fighting them off.
Superpower Lottery: Using the character editor, it's possible to make a hero with any combination of powers you want. Think about that for a minute... Though, if you make a hero too powerful, their Prestige point cost will probably be too high for you to use them in the game.
Telephone Polearm: At a certain strength level, characters could rip poles right out of the ground and swing them.
Victory Is Boring: The entire reason for the plot. Lord Dominion is so bored with ruling the entire universe that, instead of simply steamrolling over the last planet he doesn't rule (Earth, of course), for lulz he dumps a bunch of Green Rocks on it so bad people will develop superpowers and trash the place.
Video Game Cruelty Potential: You can run up and smack pretty much every civilian, who go flying away with a hilariously pathetic scream. Bonus points if they hit a building and cause it to collapse.
The only downside is that civilian kills and building collapses will count against your Prestige for completing objectives and your villain kills, which is spent to recruit optional heroes during the campaign. And considering that you can get "Robot Killer" Man O'War and "Lil' Mook Destroyer" Bullet this way, it's best left to skirmish.
Fun fact: For some reason, picking up a car that just drove up to you and stopped (clearly implying that there was a driver inside) and throwing it at other cars (which also presumably have drivers inside) has no impact on your prestige at all. Have fun!
Useless Useful Superpower: Abilities like Tunnel Travel and Teleport Self are really useful to bypass obstacles and get in good positions for boss battles, but little else.
Plenty of Active Defences guard against only one or two types of attacks, often ones the characters resist anyway.
Weak, but Skilled: Several characters, the sidekicks Liberty Lad and Sea Urchin in particular.
What Could Have Been: There were two potential third installments in the works at one point or another. One of them (which was tentatively named "Freedom Force 3") would have taken place in The Seventies while there was another project on the board which would have given the franchise a Ultimate Universe treatment set in the present day. Both projects were put aside because of a combination of factors, including the reduced sales of the sequel as well as needing more time to work on development for a little game called...BioShock. While Ken Levine hasn't completely closed the door on another Freedom Force, he's admitted it definitely won't be coming anytime soon.
Back when the original game was in its later development stages, Irrational made some comments indicating the plan was a series of three games, each based on one Age in comics.