<p>Using a thermoplastic MDF printer with a 0.4mm extruder nozzle, I frequently have trouble with the nozzle getting clogged.</p>

<p>I am not sure what's causing the clog, but my guesses are dust and/or burnt filament (from leaving the hot end on without extruding).</p>

<p>What can I do to prevent, or at least minimize, the extruder nozzle getting clogged?</p>

<p>Bonus question: What other common causes of clogs are there? (ie what should I watch out for besides dust and leaving the hot end on?)</p>

Lubricating the filament is the most common solution I've heard of to stop filament jams and clogs. Lubricating makes for a smoother ride through the print head. While you're at it, make sure that the filament is clean. The best way to stop jams from dust is to get rid of the dust in the first place.
Some people recommend
canola oil
, which I've heard works reasonably well for both ABS and PLA (though especially for PLA). You can even
3D-print dust filters/lubricators
, if you think this could be a serious issue.
I personally try to clean the print head regularly, after every couple prints or even after each print, if I have time. Something sharp, like tweezers, can pick off bits of filament near the tip of the nozzle. I haven't tried other utensils yet, but there are certainly other tools that would work. I've also heard of people regulating temperature with a fan, in order to prevent partially melted bits of filament clogging up the inside of the nozzle, but I don't know if that's effective.
In some cases, the problem could even be as mundane as a support issue. I once set up a spool of filament, only to have a jam when the support for the spool failed, leaving the line of filament tugging at the nozzle and clogging it. Taking steps to prevent this from happening can be simply and effective. Whatever the cause, preventative measures are always my choice.