Note the Arduino Yun's CPU is covered by a metal RF shield. I chose not to remove this shield and measured temperature of the shield directly above the CPU.
Another interesting result is the Beaglebone Black compared to the Raspberry Pi model B. Although the Beaglebone Black has better performance and power consumption, it appears to come with a trade off of noticeably higher temperatures (about 5°C / 10°F higher).
Most of the boards run at or below 40°C / 104°F which is not excessively higher than ambient temperature (about 22°C / 72°F at the time of these tests).