It means something like "all right", but it is more formal. To me, it means "correct" or "as it should be". It sounds official to me-you have to have your papers in order if you want to get a visa or work permit.

Hi, I agree with Scott, and another example is when someone dies, people will say; S/he had everything in order. Meaning the person made a will and was preparing for their death or transition. All their property and finances, etc. were in their will or designated to others after they die. This is a very common statement.