I have been using the Equal Temperament setting on the Cleartune tuner, and although it works better than my other tuners there were still some issues with intonation, and on a good day I got better results with my ear. (My ability to tune precisely by ear comes and goes, not sure why, but that's another thread...)
I tried a couple of other temperaments and with my instruments (banjos and guitars) the Almost-equal setting (in the Well Tempered section) sounds better, especially if I am playing C and D chords. I would like to try some others, but trying to remember which one sounds better in relation to others is mind boggling, so I'm throwing it out here to see if anyone else has done some experimenting and what has worked for them.