I have been testing out some of my flutes and some are within about 5-10 cents of true but some are out by 20 cents (most being sharp).
How far out is considered too far?
Also, if your flute is going to be off pitch (which in some measure it will be), is sharp or flat going to better/less noticeable?
Before answering, I’d want to know how you measured the tuning. If you just used a tuner, I’d be worried that you might be accidently manipulating the results. I’d suggest you record the scales without looking, then play them back into a tuner, so you can be sure you are getting realistic results. Ideally, I’d use RTTA, so you can play tunes, intervals etc.
Assuming you are getting reliable measurements, I’d think 5 to 10 cents is very good, with 20 being on the edge.
There is an adage that better for a flute player to be sharp than flat. I’m not sure of any scientific study into that though.
Terry
I was using some software that will record the pitch on a graph and give me the average as well. I can play a tune and look at the results afterward, but I think it only records the last instance of that note. The software is AP Tuner.
Mostly I was just doing one note at a time. I can look away and it will record the final sound of the note. Probably not as good as RTTA but I can’t be bothered to install that and I am not nearly good enough to send anyone a sound file. 
On the D flute I have been using and enjoying the most I thought it sounded quite good against the piano. I have a very good ear for tuning. But once I tested it I was about 20-25 cents sharp on almost all notes. Of course, I can roll the flute, change embouchure, but I don’t want to have to do that.
I actually had made one with the measurements from Doug Tipple’s site and dang nabbit, doesn’t it show only as much as 15 cents out. But it is flat and I seem to prefer the one that is technically sharp.
RTTA is easy to set up and use. I encourage you to try it, Darren.
In my limited experience using RTTA, there’s a big difference between playing a notes or scales (either on a tuner or on RTTA) and having RTTA analyze the notes played in a tune. I’d trust more highly the readings I get from playing notes in a tune.
I also find it surprising that from one day to the next, my playing can differ markedly. I wonder if others find that their playing varies much? Perhaps there is no way to precisely determine the tuning of an instrument, but there are relatively consistent patterns.
Keep coming back. 
Well, I meant that I didn’t want to do so excessively.
OK, I feel better now. I didn’t want to be the one to break the bad news to you.
It’s possible to get the tuning really good on an instrument you’re making/designing without RTTA or relying on having a good ear, just by using a standard tuner. But there’s a method to how to use the tuner:
Play alternately 2 different notes eg. G and A, watching what way the tuner moves and by how much as you change backwards and forwards between them. So you now know A is 10 cents sharp or whatever compared to G. Repeat with lots of other pairs of notes, until you’ve built up a picture of the whole instrument.
This takes quite a while but will give results that match very closely with what you’ll get using RTTA.
Cheers
Graeme
Graeme, how long do you hold each note? Just long enough for the tuner to respond steadily? With what kind/brand of tuner have you had success with that method?
Actually probably slightly less time than for the needle to become steady! Because if it’s become steady you’re probably altering it! I’d do about 20 notes in 10 seconds back and forwards eg 10 Gs 10 As. I’ve used this successfully with a Korg CA-30 and with the tuner on the computer http://www1.ocn.ne.jp/~tuner/tuner_e.html With the computer you can alter the speed of respose/dampening or something.
Results of whistles I’ve built, and flutes I’ve retuned by this method agree very well when played and looked at with RTTA. But RTTA is a lot faster if you’re looking at the whole instrument, plus RTTA is probably a bit more accurate. I still use the tuner and alternating notes when I’m just fixing one crook note…
Cheers
Graeme
Thanks, Graeme, that helps!