There have been a shedload of threads about the above - I just read most of them. Two of the issues I discuss below seem not to have been dealt with, and one has been answered definitively (by Rick Fielding) but it bears repeating.

Capos (Rick Fielding is God!).
1. Capo as close to the fret as possible, never more than 1 mm away. That way with luck you pull the string ONLY to the fret and do not clamp it to the fingerboard and so pull it sharp.
2. Groove the rubber on the capo where the "fat" strings are. Rick recommended bottom E and A, but I think it may be worth trying D and maybe the G as well unless you play a unison G pair
3. Never put the capo tighter than is needed to get the strings down to the fret.

Saddle Compensation - and maybe a different answer.
1. I assume we all understand the concept of the B compensated saddle. Because the B string is thicker than the top E, there is stiffness in it as it passes the saddle (Buzz Felten applies a similar principe at the nut) so the vibration in the string behaves as if the node in the string (the non-vibrating point, in this case the non-vibrating endpoint) were slightly further up the string. IE the string behaves as if it is shorter than it really is. So it goes sharp as fretted and can be observably out at the octave. So the saddle is shaved back or angled to make the string a bit longer than the simple maths would say it ought to be, in order to compensate for this "end-effect". Similarly, as the saddle is angled, it compensates for the bottom E being thicker than the A which is thicker than the D which is thicker than a wound G.
2. Now think about a 12 string. Apart from the B and top E, every pair of strings is one thin one and one thick one. So, as you fret the strings, as you move up the fretboard, the thicker one gets slowly more sharp. Hence special 12 string compensated saddles with tiny compensated bits for each string - and a problem if there need to be grooves in the saddle to line the string up. So there's the problem. Is there another way to reduce it? I have just put a set of so-called "piano-end" strings on my 12. They are Rotosound Country Golds. The winding does not come all the way to the bridge, so the wound strings are thinner as they go over the saddle, and, I guess, the end effect is less. Moreover, a string not wound all the way to the end would go out of tune anyway as you fretted it, because the mass/length ratio of the unfretted part would change. So I'm guessing there may be a heavy bit of the winding, near the end where the winding stops - which in turn would make the string vibrate more at the heavy point and so reduce the end effect. I'm still at the "It's got new strings on and will it ever get back to stable tuning?" stage so I can't say I'm really conducting an experiment yet, but does anyone else have a view on the theory?

String Tension/tuning.
Plenty of people tune down to reduce stress on the guitar. I was playing 11s on my 12, but in E flat (ie one step or semitone down). I have put 10s on and brought it up to concert. I'm sure I've seen charts somewhere that show you what the tension is of a string of a given diameter at a given pitch at a given scale length, but now that I want one, can I find it? Does anyone either know where I can find a chart like that, or know for sure whether a 10 in E is tighter than an 11 in E flat. I reckon I could probably work out the engineering math of it, because the mass per unit length will go up as the square of the diameter, and I must have an old engineering textbook here somewhere about spring vibrations (probably the chapter after pendulums) but a ready made answer would be easier and less open to doubt...