What time zone is used for operating an airplane?
The pilot (and the ATC) use the UTC (Coordinated Universal Time). The flight's departure and arrival are in terms of the local times at the respective airports.

As for data logging, the FDR/CVR usually records in UTC (preferred) or the relative time count (usually count increments each 4 seconds of system operation). See Appendix M to Part 121 - Airplane Flight Recorder Specifications, for example.