Different features are are really important to different folks. Billing, payments, invoicing, are ways your software interfaces with your customer. Then there's record keeping, tax planning, asset management and profit and loss statements. Those are metrics for your business. There are hundreds of options and as stated here Quickbooks is the 500lb gorilla and if you have an accountant they're probably familiar with it.
I wrote a blog post covering some of the existing and up and comers if want to just see a quick rundown and pricing info for things like freshbooks, jobber etc.