I try not to compare courses because it's impossible unless you play them all 100 times or so. I base my own opinion on how I felt walking off the 18th green and of course some are are "better" than others but comparing the Old Course to say, ANGC, isn't fair.
I have personal ratings of the best Dye course, the best links course, the best Dick Wilson, RTJ, Fazio, Thompson, etc. but find it difficult to compare different categories. I have played only one Doak course (last two days) and even though it is next to Muirfield I don't think anyone can fairly compare courses built so far apart era-wise. It was superb to see Tom's treatment, and nice use of trees!.
I prefer the late August version of the Old Course to any other time of the year.
Whats the best way to compare courses? Personally.