Tuning, Intonation, the Hard D and Related Concerns
As you play from B down the scale to D, the column of air inside your flute gets longer. In order for the D to come out at the same volume and in-tune-ness of the B, the air down there at the bottom of the flute has to be moving at the same intensity as it is up around the second hole when you're playing B. In other words, the lower notes in each octave need to be blown harder, and the higher notes need to blown softer. This is especially necessary in the second octave - the high A and B can go really sharp unless you're careful. Remember that the change into the higher octave should be accomplished by raising your airstream, i.e. blowing a little more across the embouchure hole than into it. Counterintuitive though it may be, the second octave in general needs to be blown more softly than the lower.
Try this: play a long G in the lower octave. Make it the most beautiful, perfect G you can play. Just hang out with the note for a while, ten or fifteen minutes. Focus deeply on the sound you're making. When you've achieved the most achingly lovely G in the history of the universe, play G, then A. Work back and forth between the two notes, making the tone and relative tuning of your A match your G exactly. (Work with an electronic tuner.) This is worth taking several days over. Then you can go on to matching your A to your B, and then your F-sharp to your G, and so on down the scale. Strive to play each note with the same beautiful tone, and exactly in relative tune. You can work the second octave this way too, though you may find it's better to start from middle D and work your way up. Also, work on matching between octaves. Work hard on all of this for at least twenty years.
The low D on some 19th-century flutes can be extremely flat - you have to give it some muscle to make it work. This technique is informed by aesthetics as much as by necessity, as it's analogous to the hard D used by uilleann pipers. A lot of Irish players really blast away at the note. Even if there's absolutely no way in the world the D can be brought up to pitch, the listener's attention can often be diverted away from your intonation by the ferocity of your attack. (I'm kidding, of course.)(Mostly.)
If your octaves seem wildly out of tune with each other, you may need to check the adjustment of your headjoint cork. Under normal circumstances, the distance from the face of the cork to the center of the embouchure hole should equal the diameter of the headjoint's bore. Increasing the distance will flatten the second octave; decreasing the distance will sharpen it. You can check this measurement by marking the diameter on a dowel, wooden spoon handle, or your cleaning rod, then seeing if the the mark is in the center of the embouchure hole when the dowel is touching the cork.
When playing with other people, many flute players prefer to tune to G. The trouble with this is that once you have the G in tune, you have to adjust the B and the A downwards while playing, which to me is more difficult than adjusting the low notes up. I find I have an easier time playing with good intonation when I tune to A. Your mileage, of course, may vary. Whichever note you tune to, it's very important to listen closely at all times to your playing to make sure that you're in tune, both with yourself and the people you're playing with. The tuning slide can only make you approximately in tune - the rest of the work has to come from adjusting your breath and embouchure as you play.