As a fountain pen user, I've always heard about precautions you must take before you board the flight. Most people I spoke with recommend to clean the pen completely or, if you really want to use it, keep it fully inked as to minimize possibility of air expanding and pushing the ink out.
On the first glance, all this seems logical so I always took precautions. Considering that all my flights lately have been cross-Atlantic, it seemed as a wise choice. However, on my last flight I decided to experiment a little.
On my trip from USA to Croatia (Seattle-Frankfurt-Zagreb) I carried four of my pens: Pilot Custom 74, TWSBI Diamond 580, Platinum Cool, and Pilot Metropolitan. Custom 74 was attached to my notebook while remaining pens had home in the case located in my backpack. All were fully loaded with different inks: Noodler’s Heart of Darkness, Diamine Oxblood, Private Reserve DC Supershow Violet, and Private Reserve Sherwood Green respectively.
I used Custom 74 with Noodler's during the whole flight and, outside of the nib creep Noodler is famous for, I had no issues what-so-ever. And yes, I used it both during take off and landing - just to be sure. Other pens I took just a few scribbles with for test purposes but I haven't noticed anything wrong.
On the way back I expected slightly different results as I have used some ink and didn't refill any pen. Custom 74 was close to being empty, TWSBI was around 50%, while Cool and Metropolitan were reasonably full at around 75%. I expected trouble.
Surprisingly, nothing happened. My pens operated just fine with TWSBI taking more of an main pen role from Custom 74. Absolutely no leakage occurred during any of two flights (Zagreb-Frankfurt-Seattle).
Based on my, admittedly limited, test I don't see any justification of additional pen preparation before the flight if you are bringing it in cabin with you. Any pressure change in the cabin during flight is small enough that any modern fountain pen can handle it just fine. Yes, in the case of sudden decompression, pen would probably leak but then you'd have more important things to worry about than 2 mL of ink.
If you are transporting pen in unpressurized cargo area I would always go with cleaning out the pen completely. In all other cases relax and write on. :)