I've experienced many self-proclaimed agile teams and lean startups. While there are many approaches for development and business functions, there are few to none for organizations and team management.
I have no grounds to say that I know the best practices, but I wanted to start the conversation with this document and see where the community takes it!
Check out "The Founder's Dilemmas" by Noam Wasserman. Lots of great tips based on a huge dataset of startups.