We are using trello. Our startup is a travel planning & tracking app with web and mobile apps. Two of us are building it so we have kept it very simple. We have a "features" track/list, 3 tracks for API server/Infrastructure TODO, Web APP TODO and Mobile TODO, and two tracks for "Doing" and "Done". We are still developing so no bug management yet but in future I would keep it separate from trello. Maybe google docs for simplicity initially.