My business is run on a cash basis so I just use Quicken to track deposits and print checks. It generates a good tax report which I print out and hand over to my accountant.
All my invoicing, Purchase Orders, Order Acknowlegements etc. I do in FileMaker Pro. Since my ad specialty business requires tracking customer/vendor contact information, invoicing, shipping and sales tax information along with artwork and imprint information, I found that FMP was the only thing that would let me combine all this on one form so I wrote a custom database to meet the need.