The hot end is one of the most important parts of a 3D printer, and also one of the most troublesome. The thermal dynamics of a hot end are very critical, and if everything isn't perfect, they just won't work. I am by no means an expert on the subject, but I've had my fair share of issues, so hopefully my experiences can be of help to others. Here are some of the issues I've had and how I fixed them. This post deals specifically with J-Heads, but most of the tips apply to other hot ends as well.
Cooling
I'll start with something extremely important and also easy to fix. With hot ends like the J-Head, active cooling is a must. You need to have a fan blowing across the PEEK barrel of the hot end to prevent heat from travelling up from the heater block. Without this, jams will occur due to the fact that the plastic is melting too far above the heater block. If you do not have a fan and are having jams, simply add a 30mm or 40mm fan to your hot end. There are plenty of mounts available for download, or you can design your own. In addition, make sure that you insulate your heater block with kapton tape or another insulating material like fiberglass. This will help to keep the heat in the heater block and stop it from creeping up the barrel of your hot end.
Plug Formation
This is a big problem with cheap J-Head clones, and has been an issue with every J-Head I have bought off of eBay (if you buy a real J-Head I doubt you will have to worry about this). The problem here is that in knock-off J-Heads, the set screw or pneumatic fitting that screws into the top does not push down on the PTFE liner tube. When you try to use the hot end, the melted plastic expands and pushes the liner tube upwards, filling the space beneath it. This creates a plug which stops the filament from coming out of the nozzle. This problem is also easily remedied: simply add a spacer between the set screw and the liner tube. M3 nuts are the perfect size and work well. I place two on top of the liner tube and then screw in the pneumatic fitting, making sure that it pushes on the nuts and that the threads don't bottom out first.
Unidentifiable Blockages
Sometimes a hot end doesn't work and there is no obvious reason. There could be debris in the nozzle, or something else that you are not aware of. In these cases I've found it best to clean out the nozzle by using a very thin guitar string. Heat up the hot end and then thread the string through the nozzle, running it back and forth to clean out any debris. Even when there is no obvious blockage removed, this can help. I've had hot ends start working after doing this even though I never actually diagnosed the problem.
Temperatures
Try a few different temperatures if your hot end refuses to extrude. It's possible that you are running too hot or too cold, both of which can lead to jamming. You can't always trust recommended temperatures. Filament is not all the same, and neither are thermistors. For example, many manufacturers recommend printing PLA at 170 degrees and up, however we sometimes print at 165 degrees and can extrude at as low as 145 degrees. This is most likely because our thermistor is not completely accurate. This won't cause problems as long as it is consistent, but it means that you can't always go by what other people are doing, because not every machine is the same. So experiment and see if changing the temperature can make your hot end start working.
Conclusion
That basically sums up all of the advice I have for solving hot end jams, specifically with J-Heads. I'm sure that there are many other issues that I didn't cover, but hopefully this can help people who experience similar issues to what I faced. I have found that once a hot end is working properly it gives me very little trouble. Happy printing!