I ran a poll today, and the same poll 18 months ago, just after the last book in the trilogy had been published. The results are shown below:
The sample sizes (~200 in each case) mean that the differences are statistically significant, but that there are quite a few % points of error possible here, so the true difference may be a fair bit smaller (or larger) than shown.
"Best" is a harsh and artificial choice but it's interesting to see nonetheless.
Possible reasons for the change?
i) 18 months ago most readers had waited between books and just recently read the last one.
ii) Today many readers may have read all three books in a week/month.
iii) The average time since reading the books is likely to have increased, meaning the judgement may be based more on a collection of stand-out scenes rather than the detailed plot/feel of the books.
Really the books should be judged by what they're trying to achieve and the context they're in. Prince of Thorns I like for its pace and for capturing that raw, immature, bridge-burning, defiant, hurt, and dangerous younger side of Jorg. King of Thorns I like for the twisty-ness of the timeline, the interdependence of the threads, the passion of the ending, and the growth in our protagonist. And Emperor I like for its sense of focusing down: on a place, on a time, on a person, and for the fact it brought about an ending which I felt held up rather than let down what had come before.