For Wonder Woman my favorite is easily The Legend of Wonder Woman. It's one of the best modern origin stories to date (I prefer it over her Year One).

Superman Birthright is the best Superman story I've read to date, but the recent Man and Superman deserves to be read as a new classic too in my opinion.

Most of the Batman stories I've read have already been mentioned. Batman Prey, Batman vs the Monster Men, and Batman vs the Mad Monk are worthy reads, don't think they were mentioned. I will note I prefer Zero Year over Year One as far as origins go. Blasphemy I know.

Just stuff off the top of my head.