Practicing intonation, I've noticed a few funny quirks of mine which I know are shared by many other flutists, so I think it is worthwhile confessing and hanging them out to dry.
(By the way, barring any live musicians I can scare up to do my nerdy exercises, my partner in intonation practice is my Korg OT-12. It's a bit chunky and pricey, but it offers decent range of sound output. It is also recommended by orchestral piccoloists for its good registration of high pitches.)
But first I need to get another pet peeve off my chest: flutonation. It's the natural intonation of the flute. I often hear it when a flutist is playing a solo piece without accompaniment, esp. a contemporary (atonal) piece that they think doesn't need to be in tune. Oh boy....eyes rolling.....
I admit that I have flutonation in spades: C# too sharp, low and mid Eb too flat, but the high Eb too sharp. This is why I hate hearing it in other players :-)
Now for those other quirks:
When tuning unisons, I notice I tend to tune just a few cents sharp. I realized why after awhile: when perfectly in tune with my OT-12, the sound of the OT-12 disappears completely! The harmonic structures are so interlocked that they are indistinguishable. If I'm a little sharp though, I can still hear the tuner. And in my quest to always listen, to play so I can hear my partner (even if mechanical), I play so that both can be heard. Funny, huh? A case where overdoing one aspect can mess you up in another area. Sort of opposite the way pitch rises in orchestra - where you play sharp so you can hear yourself.
Another thing is octaves. I can tune vertical octaves without any silliness, but melodic (horizontal) octaves are another story. They are almost always too wide. I don't know why, maybe I have played the flute too long and have a severe case of octave flutonation. Then there is picctonation. I hear octaves on the piccolo too narrow. That's probably because I like to play with the cork rather close to the embouchure hole - but still, I should know better. I really have to re-train my ears with a fixed pitch instrument or my korg. I've developed some exercises for octaves with my korg that involve listening, not looking at the blinking lights.
In general, I've got several exercises for tuning with a tuner that involve listening to combination tones, complete with explanations. They are no longer publicly on my site because I am considering publication, but- if someone is really interested I can send them pdf.