Fruitful Time makes a free Productivity Meter that we’ve mentioned before. It tracks how your computer is being used and gives you a good idea how your time is being spent. They now have a paid Business Edition that lets you do the same thing for a group of employees. I have used some tools like this in the past so my staff could tell where they are spending their time. It looks like it is still windows only. For a cross platform (OSX and Windows) tool, check out Slife. They make a similar free personal/paid team product.
If you are looking at a product like this, one of the big things you want is the ability to track things based on the path or name of the document being used. So clients/XYZcorp/document.txt would accrue time toward XYZcorp and /ABCinc/document.txt would count toward ABCinc. It sounds like Fruitful Time can handle the document name which would work if you named everything with the client’s name at the beginning.