Far Cry/WMG

The Jackal's real name...
...is Jack Carver. Think about it; both are arms dealers, have unusual tastes in clothing (Jack's Hawaiian, Jackal's native shirt), and started off in the Navy. The few times you show up in the aftermath of a Jackal attack the scenery shows damage in excess of what you can inflict on it, as well as amounts of corpses you'd have trouble creating alone, possible showing that the Jackal has superhuman strength/endurance. Also, in previous games, exposure to the super serums usually has a... negative effect on the users sanity. Obviously Jack just had a longer shelf life than the others, since the Jackal doesn't make for a poster boy for having all his marbles. Undisclosedistan, Africa just happened to be where he was when he snapped.
 * Or possibly Far Cry 2 takes place before Far Cry 1, where the Jackal takes a new name and goes into hiding.

You Are the Jackal... Who might also be Jack Carver
Throughout the game you play as a split personality of the Jackal who has no knowledge that the Jackal side is a part of him. No one recognizes you because no one has seen the Jackal, and Reubon's tapes where an interview of a fake that you hired to throw possible assassins of the trail. Everytime you see the Jackal it is actually just a hallucination and an internal conflict between the two personalities, which explains why neither of you are able to kill each other, and why the organization that sent you to kill him is never mentioned- it doesn't exist. At the end of the game you actually are able to denotate the bomb remotely, and by doing so you only "kill" the Jackal apart of your mind. You don't shoot yourself at the end, because that was just a trick from the Jackal side of your mind to try to take you down with it. As for the Jack Carver part, your incredible fighting and survival capabilities could be caused by the mutant serum. The split personalities might be a side effect as well.
 * This might explain the player character's ability to casually flip over two ton jeeps, and the fact you're unable to play as the 3 female mercs.
 * But what if you DO blow up the TNT? Does Jackal simply become the dominant part of your personality? Either way there's a gunshot as Ruben's final picture at the end of the game shows up, implying that the main character did eventually kill himself.
 * That doesn't really mean anything concrete though, especially when WMG is in play.

All the briefcase diamonds are cursed
It's like Tutankhamen's treasure - extremely valuable and unfortunately brings immensely bad luck to anybody near it. Some time in the past, before you get there, some witch doctor or tribe chieftan scattered them around the entire country in obscure locations to spread out the curse's effects, (having ten or more of the briefcase diamonds in the same place might be enough to trigger an earthquake, or a drought for example. So it's better to have them spread out). Because the player character is usually carrying around some of the diamonds, it explains why enemies are constantly shooting at him and coming after him in jeeps. This also explains why such valuable diamonds are being randomly found in the game, and why nobody else has already taken them (everybody except you knows about the curse). Also, it explains why the unnamed country is in such a bad state - by spreading around the diamonds the curse is extended to the entirety of the country, rather than just one person.


 * Also note that many of the diamonds are found near abandoned campsites, dead bodies, and/or wrecked vehicles. Even the ten diamonds you get towards the end of the prologue are said to have been stashed by a not-very-bright footsoldier who then promptly got himself shot dead in the gunfight at the start of the game. "Maybe you killed him."
 * Your buddies also meet their demise shortly after you give them a briefcase full of diamonds. Before that they didn't seem to have any, you never got a reward for doing bar quests.
 * The gun seller(s) get cursed when you use the diamonds to pay for new equipment. The Jackal is so successful because he doesn't accept diamonds as payment.

The Main Character is a Drug Addict
Unless he's got that fastest on-setting case of malaria ever, this seems likely- he was implied to have only been in Africa for a few hours before he suddenly keels over with it. In reality, he's a drug addict, and the malaria attacks are withdrawal kicking in.


 * Those must be some freaky antimalarial pills the locals rely on, then.