I see that Prayer Lists are not mentioned in the Beta Release notes as an LDLS3 feature that is planned to not be supported. Neither do I see it implemented.
Please don't ditch this feature. With syncing across computers (and iPhone syncing), prayer lists would be an extremely powerful part of our lives. Imagine you tell somebody you'll pray for them, pull out your iPhone, iPod touch, or hopefully Blackberry and put legs to that promise.
Then integrating prayer lists in this dynamic way would only encourage users to make Logos a part of their daily devotional time. This would be a good thing for existing users, and it would also meet a need for the average user who doesn't think that they would benefit from all the powerful search features of Logos. Those guys just want a Bible, some highlighters, a place to take notes, and a commentary or two maybe. They get all that with a Bible and a piece of paper...a robust, syncing prayer list feature would only serve to help them see the benefit of integrating a digital library in with their devotions (on their phone or computer).
Prayer Lists (along with reading plans and devotional books) have historically been one of the major selling points to the dozens of people that I have talked into making an investment in Logos.
All that to say...Please give us a prayer list feature...