For B-B oriented small businesses or those that sell complex products and / or services for which you need to create proposals or estimates, track billable hours, or keep track of deductions based on a retainer:

Harvest App: simple and easy to use yet quite flexible (works directly with Stripe and Paypal).

17hats: way more than invoicing so could be overkill but definitely worth a look—you may not know what you are missing.

Freshbooks: also more than invoicing; especially good if you want WordPress integration via Gravity Forms, whereby you can turn an intake form into a configurable product or service invoice directly in Freshbooks—a nice time saver which also eliminates errors in transcribing.