I totally agree with the problems Daniel is mentioning. After being increasingly frustrated with most solutions available, we created an iOS app that attempts to solve exactly those problems. You tell the app how long a tasks will take, when it needs to be done and how important it is. Our app then selects the tasks with the highest priority for you every day. It's called Finido: www.finido-app.com
I am curious what you guys think! Is it a solution to the problems described by Daniel?