A-Team Firing: Most NPCs are hilariously poor shots, especially low-level cartel grunts and bandits. It's perfectly possible to win a fight by standing perfectly still in the middle of an open field picking people off while everyone sprays inaccurate machine gun fire in your direction for five straight minutes.
Anyone Can Die: Almost every character in the game world can be killed at any time, for any reason. Collateral casualties are frequently common in faction fights, and there's nothing stopping the player from walking up to civilians, shopkeepers, or quest givers and shooting them in the face.
Artificial Stupidity: The game's AI wasn't bad by 2005 standards, especially considering the size and complexity of the game world it had to navigate, but it's still nothing special, and has occasional moments of true stupidity (faction battles will occasionally consist of two groups of guys standing in a line three feet away from each other and shooting randomly until everyone dies, for example).
Banana Republic: Realia. The game is a pretty good walkthrough of this trope.
Chekhov's Gunman / The Dog Was the Mastermind: In the bar near the very beginning of the game, you can have an extended conversation with a wealthy philosopher. He has unique dialogue and more lines than the usual NPC, but there's otherwise nothing to suggest he's related to the main plot. it turns out he's the Big Bad. Indeed, it's very easy to miss speaking to him entirely since he's surrounded by non-important signpost-dialogue NPCs, which makes The Reveal much less dramatic.
Everything Trying to Kill You: Snakes, killer insect swarms, super-persistent jaguars, the locals, traffic, even factions duking it out between themselves are no strangers to putting a few bullet holes into your car if you drive down the wrong road.
Friendly Fireproof: Totally averted, which makes large firefights doubly dangerous - not only will your enemies try to kill you, you can also take damage from your allies' stray shots. There's nothing quite like accidentally getting shot in the head by one of your squadmates, or getting pureed by a poorly-aimed gunship cannon burst.
Gatling Good : The only gatling guns in this game are static AA guns and the front cannons of gunships. A hand held model would have been nice though.
Global Currency: Partial aversion. While almost all the towns and merchants in the game use Realian pesos as currency, the native tribes pay you in jewelry and idols instead of money. It's totally worthless outside of the native villages unless you take it to an antiques dealer who will buy it from you.
Grey and Grey Morality: There are no good guys in this game, although the Mafia and Bandit factions are somewhat more dickish then the Well-Intentioned Extremist Government or Rebel factions. The Native American faction is interesting in that while it's considered a single faction, the faction missions are provided by three different groups: two are fairly peaceful "we just want to be left alone" groups whose missions are either peaceful or self-defensive in nature, while the other is led by a crazed, murderous "kill the White Man" cannibal who sends you out to massacre pretty much anyone he doesn't like (including tourists and fruit merchants).
The rebel agent spying on Realia's CIA station chief has a massive tricked-out listening post set up in the apartment directly underneath the station chief's apartment, so close together that they can probably hear each other talking.
It's also subverted with the CIA contact in the rebel capitol - he's 'hiding' in plain view in a house with a big, prominently-displayed American flag, and thinks he's concealed his identity quite well, but asking around reveals that everyone in the town knows he's a CIA agent. They let him continue to think he's fooling everyone because they don't want to hurt his feelings.
Noble Savage: The Realian native tribes. They're also ridiculously, offensively stereotypical caricatures of generic Native Americans in appearance, behavior, and manner of speaking, to a degree that's either incredibly racist or incredibly hilarious depending on your point of view.
Not Even Bothering with the Accent: In the game's English dub, most of the characters are voiced by American voice actors who make absolutely no attempt at all to fake a Spanish/Latin American accent. It's really quite jarring, since they all address you as 'gringo' despite otherwise speaking perfect English with a US accent.
Random Encounter: All the time, not all of them hostile to you. Factions patrol their territory and mount raids on enemy territory, as well as setting up ambushes on the roads to catch enemy vehicles. This can be rather problematic if you happen to be driving on said roads, as the crossfire can potentially kill you.
Unusable Enemy Equipment: Both averted and played straight - everything an enemy is carrying can be picked up and used, but their guns are always in ridiculously poor condition and will jam or misfire constantly.