This has been asked before and there are always many suggestions to take the cheap route of $30-$40 programs. A few suggest a full accounting program. It is in my opinion a $30-$40 program is a false economy.
Whether you are doing this work as a sideline or fulltime, solo or with extra labor a full fledged accounting and payroll program will serve your needs best.
I personnally think that QuickBooks does it best after coming over from 16 years of DacEasy. Not only can it handle the billing easily but also paying your bills, tracking assets, payroll etc. It makes it easy to do your own book keeping. By organizing all expenses properly, income tax preparation is quick and easy for the accountant. I see my accountant once per year and present him with an itemized profit and loss statement, fill out a form he sends with the relevant personal info and a list of depreciable items and their costs that I purchased during the year.
My state and federal taxes including schedule C are prepared for a few hundred dollars and opposed to the many hundreds or even thousands that other spend using an invoice only method, boxes of loose records and check book registers or stubs.
Doing it my way saves me $$$$, makes desk time easier and simpler, gets the info I want and its alwasy at my fingertips.
I'm currently using QB Pro and QXpress for scheduling and life is better.