I highly recommend https://53mp.billingarm.com/signup/ (FreshBooks - Online Invoicing, Time Tracking and Expense Service) to all of my clients who are in need of billing services. As a programmer I was thinking about creating my own, and also looked into 3rd party scripts that can handle billing, invoices, files, clients, etc...but did not find any.. I ended up stumbling across freshbooks and have been with them since. Accounts are free to start, and they are always adding new features, listens to advice and recommendations, and has one of the best customer supports I've come across.

They do regular invoicing online, mailed, export to quickbooks, even accept payments online through paypal, or any of the more popular merchants.
and lets you have staff, projects, timeclocks, assign clients to staff, invoice dispute, file transfer, and a lot more..
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but seriously.. check it out https://53mp.billingarm.com/signup/ it's completely free to start

edit: I just saw someone else recommended it as well