http://www.bioinformatics.org/sms2/
The Sequence Manipulation Suite 2: a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences.
http://tools.neb.com/NEBcutter2/index.php
This tool will take a DNA sequence and find and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once.
http://www.bioinformatics.org/sms2/