[ska]

In the past I've used emacs org-mode to do time tracking against particular projects with breakdown level you can easily control. This can be used to produce summary tables in a variety of ways, which I usually cleaned up a little before plugging into an invoice (typically monthly or by project, sometimes more often). They don't have to be pretty, just accurate.

I've also used an accounting system like xero which will generate invoices and give payment options, but that was more about the back end matching an accountant's system.