Certainly, as far as guitar goes, I've seen two different methods of tracking (among the multitude of others). One using white noise to line up capsules, find the deepest null etc, all pretty standard. I've also seen a method where you put the mics where they sound good individually, and line them up in tools using aux channels and the TimeAdjuster plugin (along with an obvious transient to find the delay between mics/amps in samples) summing the result to single channels in tools. Specifically, this was with a dynamic close to one speaker, a condenser about a foot or so back from another (top 2 of a 4x12 in this case) to get a little more of the 'whole cab' sound, rather than just ear to one cone, with a total of 3 cabs, each fed by a different head, all fed by one guitar signal. I've seen the TA method used to line up inside, outside, and sub kick mics as well.
I've seen both methods used in the same studio, heard the results of both, and find both to be interesting methods for use. Not necessarily saying one is better than the other, but food for thought, certainly. Anyone else use the TA method? It's one that had not occurred to me before, the phase alignment method is generally the 'taught' method. I've found myself using it more often recently, with good results, especially if using a multiple amp setup. The slightly computational, mathematical element of working out samples between mics, and then amps, and them combining them to one track makes a lot of sense to me. I find I can get my head around it fairly easily, and it certainly doesn't sound bad. Certainly, a multi mic/amp setup would be a nightmare with phase, although I suppose no more than with time alignment.
Equally, any people have experience with the whole 'phase eq' thing mentioned in the tracking guitar article that was in SOS a while back. I think it was Joe Baressi (two r's, one s?) who is mentioned as being a fan of the technique. It's something I've never really got around to trying, so I'd be interested in knowing if people have had success with it.
Vaguely related, the whole overheads equal distance to snare thing. Is it necessary? I've come around to the idea that it doesn't really matter so much. The differences in time between the two microphones are what make it stereo in the first place, are they not? I tend to have close mics anyway, so if I need something to be bang in the centre, the close mic is there. Again, not saying a method is better, just interested in opinions on it. Healthy discussion, and all that jazz.
Apologies for the word-splurge, just a thought that popped into my head, thought it was worth opening some kind of discourse on it.