(Author of the blog post here)

We use the scoring function published by Hsu et al[1], which most scientists seem to be using. This function takes into account both the number of mismatches and where they occur in the guide. There's a more readable version here: http://crispr.mit.edu/about .

[1] http://www.nature.com/nbt/journal/v31/n9/full/nbt.2647.html