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.
An excellent explanation of employee monitoring, why it is needed and how FruitfulTime ProductivityMeter Business Edition helps you as a manager or an employer can be seen at: http://www.youtube.com/watch?v=rCWdu-N9InU