There are 2 main ones I've used:
Zhang lab (MIT) CRISPR design site
For identification of standard 23-base targets, scored by a metric that minimizes likelihood of off-target cleavage. Also for locating paired targets for paired-nickase approach.
ZiFit
From the Zinc Finger Consortium; originally for zinc finger & TALEN target screening, adapted for CRISPR . Allows identification of shorter targets for the truncated-target approach.
