ChargeOver - ChargeOver automates recurring billing, subscription billing, & payment acceptance. A SaaS that integrates with Xero, Quickbooks, & has an API. Free trial.
InvoiceNeko - An open-source and free invoicing system
MinuteDock - Web-based time tracking software designed to integrate with the Xero accounting package.
Invoice Template - Create beautiful looking invoices in seconds
fusebill - Fusebill is the leading recurring billing and subscription management software for businesses. Try Fusebill for subscription billing made easy!
Invoice.app for Mac - Invoices made easy