When I was down there, a buddy and I spent some time researching exactly what it would take to cross the Gap on foot. We have a high danger tolerance, and I'm always deeply skeptical of advice that seems to be written for the prototypical dumb tourist.
Nevertheless, after talking to a number of locals (including some that volunteered to guide us) and spending some time in a couple Darién villages south of Yaviza, we decided against the trip.
The first thing is that the danger level varies considerably with time. The FARC is not nearly as strong as they once were, but they're getting desperate - in the previous two weeks of my visit, they had crossed into Panamanian territory twice to hold up general stores. Desperate, hungry people with guns. But that was two years ago - it might be more quiet now.
We had a fantastic time going into the jungle by boat on two occasions; one a couple hours in to a village that was throwing a big party, and another about four hours in to Union Choco where we were a guest of the regional judge (who we had met at the party). Unfortunately the morning after our first night in UC (staying in the hut that Trujillo used to use when he helicoptered into UC "to think"), a couple Panamanian soldiers knocked on our door at 6am and informed us that they had orders to "take us to Yaviza". No more information, the judge had no idea what was going on, and phone calls to Yaviza (from the single phone in town) could shed no more light on the subject.
When we got back to Yaviza, we found the Panamanian army mobilizing in secret - they were basically starting a war and didn't want us in the way. UC was pretty far from the front line but apparently there was a CIA advisor present who didn't want any Americans seeing him. Shrug.
So... this is how it is. If you try to cross the gap, you have to hide from *everyone* - the FARC, the drug smugglers, the Panamanians, and hell, maybe even the CIA. It might be super dangerous, it might be just mildly dangerous, but there's no way to tell until there are guns pointed at you. It just wasn't worth the risk.
I will say, though, that we had a fantastic time going to Darién villages. It really feels like the wild west down there; a strange mix of huts on stilts, topless natives, cockfights, and haggling over how many gallons of gasoline it will take to get upriver. One of the highlights of my year on the road. Just go to Yaviza and ask what's going on. If you're lucky you can catch a cheap ride on a boat hauling ice or