Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Doench et al, Nat Biotechnol. 2014 Sep 3. doi: 10.1038/nbt.3026. [Epub ahead of print].
Second, they of course have made their scoring algorithm available as a web tool: http://www.broadinstitute.org/rnai/public/analysis-tools/sgrna-design
I took a crack at it with a small DNA sequence from mouse that I know has a decent CRISPR target. Interestingly, my pre-validated target had a lousy score (~0.05 on a scale from 0 to 1) despite my knowledge that it works pretty well in my hands. I take this to mean that of course, no scoring algorithm is perfect, but also that most targets actually fall into the so-so category of activity. This jibes with data in this paper somewhat and I won't jump to conclusions based on my N=1! I'd be interested to hear other people's results from running their targets through this algorithm.