I noticed the unmistakable X Windows "X" cursor and gray loading screen on an in-flight entertainment system that crashed on me. I think it was Virgin America, one of their early flights after they launched.
The Delta in-flight entertainment systems also (at least as of a couple years ago) seem to be Linux-based. I had one crash and reboot spontaneously while I was using it, and was greeted by a couple Tux logos and a verbose Linux 2.4 boot process when it came back up.
I used to freelance at one of the big two major IFE manufacturers. Their systems are a bit of a hodgepodge of platforms. Currently, the dominant platform is Linux, running either a) a QT based GUI or b) a HTML based GUI.
But most new planes coming off the ground today are moving to Android based systems, since they have many advantages - it's much easier to get content like games and apps, and cheaper to engineer and develop for.
One of the problems with IFE systems today is that both A380 and 787 deliveries have been significantly delayed - often the IFE hardware is just sitting in a warehouse for several years waiting for the plane to catch up to it. So by the time the plane finally is delivered to the customer the IFE system may already be 4-5 years out of date.
I helped someone sitting next to me on a flight deal with the fact that the touchscreen wasn't calibrated, you had to move your finger around and see where the cursor ended up, then start to translate your pokes a few inches. ;d