An excellent question you ask! At this time there are good billing programs and good treatment planners and good assessment tools, but few that combine even two of the options. I know that Touched (Outer Montana Systems) has a good treatment planner/biller combination, but am not sure about the assessment part. Wiley has a good treatment planner (Theracribe) and is in beta testing for an accompanying billing program, but no assessment function (i think). SOS has a good combination package that will do all three, but it involves two programs - Case Manager and Office Manager - which can be connected. Civer-Psych (Civerex Systems) also has modules that can be coupled together to do these functions.
The bottom line: You will need to try out a few systems and see which meet your needs on each front.
My future hope: Every billing program will easily link to or include all of these functions!!!