FreshBooks - The ideal accounting software for small business owners.
ChargeOver - ChargeOver automates recurring billing, subscription billing, & payment acceptance. A SaaS that integrates with Xero, Quickbooks, & has an API. Free trial.
Zoho Books - Smart Accounting for Growing Business
Elorus - A super-easy online invoicing & time tracking software
Paymo - Manage projects, track time, create invoices, and get paid online.
MinuteDock - Web-based time tracking software designed to integrate with the Xero accounting package.