I've been trying to find software to highlight epubs without success. If you have a PDF version, ezPdf and Repligo will both highlight them. The highlight stays with the PDF so it's there if you read it elsewhere. I like ezPdf a little better because it keeps the zoom setting better. But highlighting in Repligo seems to be a little easier. Ymmv.
Hopefully someone who knows how to highlight in a epub will chime in.