I built my own time tracking tool (https://logmyhours.com) for tracking my time and creating invoices for any side freelancing I was doing. I'm actually hoping to go full time on this in the next 6-12 months.

I use a bit of Trello and Freedcamp for my todos and planning.

I also use RescueTime to make sure I'm keeping productive. I'm actually exploring adding integrations with RescueTime with LogMyHours, to see how productive you were for each timesheet, and reporting period.