ChargeOver - ChargeOver automates recurring billing, subscription billing, & payment acceptance. A SaaS that integrates with Xero, Quickbooks, & has an API. Free trial.

FusionInvoice - Self hosted invoicing for freelancers and small businesses

fusebill - Fusebill is the leading recurring billing and subscription management software for businesses. Try Fusebill for subscription billing made easy!

Invoice Ninja - Invoice Ninja is a free, open-source solution for invoicing and billing customers.

MinuteDock - Web-based time tracking software designed to integrate with the Xero accounting package.

Zervant - Easy invoicing, expense management, reporting, and customer feedback.