In order to help users better, I need readable log files. Text log files (ending in .log) obtained over the CLI are frequently corrupt. They have lots of transposed data, lots of half-read lines, etc.
On PIXHAWK, binary logs are stored on the SD card, in separate files in a FAT filesystem, in .BIN format. This means you can just plug the SD card into your machine and browse the logs as if it were a USB flash drive.
On future versions of ArduCopter, log download will happen over MAVLink - this will make things easier. But for now, I'd like to see more logs to coming from the SD card, rather than the CLI.