LiquidPlanner does it right. It tracks date drift and the estimated number of hours over time. You can comment on tasks through the web interface or through email. You can have it track both your bill and pay rates. It has a simplified portal interface to give clients access.

Affiliate link: https://app.liquidplanner.com/signup_a/161/516fb8abc586ae567...

I've started developing a kanban-style project management tool (http://www.octoberswimmer.com/about/) based on huboard, but I still recommend LiquidPlanner to everyone.