First I use my ears. But to be sure:
For electrics, acoustic/electrics and basses, Boss TU12H. Still strong after 25 years.
For acoustics that don't plug in, like my D-40, dobro, uke, and mando, IntelliTune IMT500. Clips on the headstock.
Or a tuning fork on the lower bout of the body to match vibrations of various A harmonics.
The onboard tuner on my Takamine Santa FE EAC38C is pretty accurate, and so's the tuner in my Boss ME-50.
But I double check with the TU12H or IntelliTune.