Personally I label all the wires, figure out what wires are on the same windings, and ohm them out.
Then, for power transformers, generally it's easy enough to know where the input is so I'll hook up a 12VAC wallwart to the input, taking note that it's probably at 14V, and then I measure the voltage across the windings. Do some math-a-magic and bingo-bango.
For example, I read two secondary windings, 41.2ohms and 560ohms; it's likely that the 560 is your HV. Turn on the 12VAC wart, note that it's putting out 14.1VAC, and I measure 63.5VAC out on the HV lines.
120 / 14.1 = x / 63.5
(where 120 is your wall voltage)
Rearrange for x; x = (120 / 14.1) * 63.5 = 540.4VAC
These will get you close enough, think, but keep in mind that these are unloaded ratings :thmbsp:
I hope that helps! I save money buying strange iron and use 'em by this method. Let me know if anything's unclear