These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Crowning Moment of Funny: The animations. Special mention goes to seeing a tall man who scares trained soldiers to cowering and begging for their life by looking at them crooked, leaning down to have his cheek lovingly pinched by a woman who looks like your grandmother, if she'd replaced one hand with a morning star.
How you deal with many of the Super Agents, especially Mariana Mamba ( You make her fat.) and Dirk Masters ( Steroids + Laboratory bio-tanks = a freak under your control.)
Crowning Moment of Awesome: In the Ending after you conquer the world, the Evil Genius use the United Nations General Assembly Hall as his throne room where he's venerated, you really have the world in your command.
And then Exceptional Veterans go and turn it Up to Eleven from Soldier squads - they will shoot on sight, they will plant charges, and if you are not properly prepared, let's just say that they can make your life hell.
Designated Hero: The so-called "Forces of Justice". Jet Chan in particular has been known to blow up your hotel while there are tourists in it. He, Dirk Masters, and John Steele will even indiscriminately murder your non-combat minions for shits and giggles.
After the Enemy Civil War is activated, agents who had killed their fellow do-gooders from a rival agency will earn you 'heat' by taking pictures of their bodies, essentially framingyou for the act. Case file: JohnSteele
Fridge Brilliance: As detailed under Enemy Civil War on the main page, the various spy agencies are supposed to fight one another thanks to moles amongst their leaders after a certain quest. It has a notable habit of not working, with the soldiers working together on these occasions. The plotline of "special forces agents/soldiers discover their commanding officer/leader/superior is lying to them about their allies" has appeared in spy stories and political thrillers quite frequently. How many times have those soldiers figured this out, and then worked with the former enemy to take out the Big Bad?
Game Breaker: Jubei and Lord Kane, used in combination, can take out the more dangerous forces of justice, including super agents, without any danger. Kane's Smooth Operator ability renders an opponent completely helpless for a short period of time, because any opponent will mindlessly stand there and wait for Kane to walk to them and perform it. Jubei's Wind Walk allows him to teleport straight to the enemy and attack them without fear of retaliation, giving him plenty of time (if Kane has a long walk) to mow down virtually anyone with his powerful blade attacks.
Before the first mission in the game (the capture of a Maid), you can send your Mooks to steal money from everywhere on the planet with no way of retaliation from the Good Guys. It's quite possible to make all the money you need for the entire game this way, let the 'heat' (negative attention) from the Good Guys fade away, and proceed to play the game normally. A Bug-Within-A-Bug exists in this situation, because if you do the mission that has you stealing a painting during this time, that nation's Heat rating will never die down ever from that time on.
Similar to the above, you can also use this no-interference period to have minions plot (seek out missions) in every territory in the game. While your basic Mooks can't plot very well, leaving the game running for a few hours will ensure that (once you reach plot levels), you have access to every mission in the game at all times.
If an object is tagged for demolition, the wear won't fall. If said object is inaccessible, it won't be demolished. Uselss normally, but brilliant for power plants. Just make sure that the power plants have no empty tiles anywhere in them, as agents targeting that spot will come out of the floor if there is no access point.
That One Boss: Of the Super Agents, Jet Chan in particular. Jet Chan makes players scream in raw rage.
So much so that if Jet Chan shows up early on while you're building your base on the second island, you're better off just loading from your last save. Especially as Jet Chan is possibly the single most aggressive NPC in the game and will immediately assault any military minions who he sees, regardless of whether they're armed.
What about John Steele? His specialty is sneaking out of his jail cell and promptly planting explosives wherever he goes. His status as a nuisance is made worse by the fact that he can't be defeated in-game.
Base Mayhem can also cause hell by setting random items in your base on fire. Including things in sealed off areas you don't want your minions to visit like Ubertraps and Freak Triggers. Oh, and let your freaks escape the latter.
Steele is especially annoying since he rarely stays dead for very long and doesn't seem to see anything wrong with leaving the island and then coming back two minutes later.
Jet Chan is a hellacious pyro too. Worse, if you have nicely separated and closed off rooms, both tend to blow themselves up repeatedly in the chaos and get sent back to jail to escape and start the cycle over and over.