The Dorien Gap is a break in the Pan-American highway that really is as wild and untamed jungle as it gets in South/Central America. You are nuts to expect to traverse it overland. But, there is an alternative: You can sail around it from various ports in Panama (Colon, Portobello, El Porvenir, Carti) via the San Blas Islands to Cartagena (or Carpugana) in Colombia. It only takes around 3 days to cross, but most boats spend 2-3 days island hopping in the idyllic San Blas islands on the way, extending the trip. Depending on the boat, it costs between $350 and $600, most boats being $500. Hostels DO take a cut so if you can arrange with the captains directly, you will pay less.
The first thing: this is a backpacker trip. Expect it to be crowded, don't expect gourmet food, most captains/boats are doing this for cash -- you are not their best friend, it is not a luxury cruise, and many boats take more passengers than they should. Yes, it's a rough crossing, so do bring sea-sickness tablets and do actually take them if you are likely to feel ill. Also, it is BYO so plan wisely for what you'll want to drink for the whole time, including non-alcoholic drinks. Bring snacks -- there is nothing scheduled between meals.
There are lots of yachts out there: do your research on forums online and ask at the hostels. Note: if leaving from Panama, you will not see your ship until you are getting onto it. The San Blas departure area is remote (3-4 hours from Panama City), so you are committed to it in a way you aren't in Cartagena (although most people don't bother to check out the boats in Cartagena, either, though all will dock in the bay where they're visible).
Here are a list of boats that were running the trip in July 2012 with websites when I could find them:
Gypsy Moth -- quite sought after
Independence -- biggest boat doing it, 25+ people on board
Mintaka
Seeadler
Desdemona
Black Dragonfly
Ave Maria
Nani Moaina
Northern Drifter
Nacar
The first thing: this is a backpacker trip. Expect it to be crowded, don't expect gourmet food, most captains/boats are doing this for cash -- you are not their best friend, it is not a luxury cruise, and many boats take more passengers than they should. Yes, it's a rough crossing, so do bring sea-sickness tablets and do actually take them if you are likely to feel ill. Also, it is BYO so plan wisely for what you'll want to drink for the whole time, including non-alcoholic drinks. Bring snacks -- there is nothing scheduled between meals.
There are lots of yachts out there: do your research on forums online and ask at the hostels. Note: if leaving from Panama, you will not see your ship until you are getting onto it. The San Blas departure area is remote (3-4 hours from Panama City), so you are committed to it in a way you aren't in Cartagena (although most people don't bother to check out the boats in Cartagena, either, though all will dock in the bay where they're visible).
Here are a list of boats that were running the trip in July 2012 with websites when I could find them:
Gypsy Moth -- quite sought after
Independence -- biggest boat doing it, 25+ people on board
Mintaka
Seeadler
Desdemona
Black Dragonfly
Ave Maria
Nani Moaina
Northern Drifter
Nacar
Or check out this hostel in Panama: http://www.mamallena.com/sailboats.html or this hostel in Cartagena http://www.casaviena.com/sanblasisland.htm although almost any of the main hostels will be able to help you. This website may also be useful. Or this one.
Despite some websites online saying that there is a ferry, this no longer runs. From what I understand it ran for about a month in early 2012, but stopped soon after due to lack of demand.
The shorter alternative to the Cartagena route is the shorter Carpugana/Sapzurro/Puerto Obaldia trip, but be warned: there are no ATMS on either side, so bring enough cash to get yourself out if no boats are going -- it is not uncommon to get trapped there! This also does not really avoid the open water crossing, as you will likely still have to go across the Gulf of Darien by ferry in Colombia (unless you fly to/from Medellin). One regular company that runs this trip is the Darien Gapster. These shorter trips are usually around $300-$350.
Yes, motorbikes and bicycles can be transferred on the bigger boats. Expect to pay a full person's fare for the bike. It will have to be transferred to the boat by crane and go on the small river boats to get to/from land in San Blas -- most boats do not dock at either end, transfers are by speedboat/zodiac.
Yes, Fritz the Cat sank in June 2012. They are rough open seas and sailing is not without risk. Make sure you feel confident with your captain and discuss their experience.
Do bring a waterproof camera or a dry bag if you can get hold of one -- the San Blas islands are idyllic, but you have to swim to get to them.