When you setup a CQWP and point to a Links List it allows you to define a few fields of data in the output: 'Title' and 'Link' (unless you have an image as part of your link). This is fine, however we also want to provide a target value. I'm sure there's way to hack at the webpart and do something creative with the XSL, however I've come up with a much simpler method using a calculated field.