Really helps when we know what you want to include on your invoice, but really you could do it in any word processor, excel, I like quickbooks because it keeps everything in one place, I have used Invoices2Go, Google is your friend.
I use QuickBooks so I just print the invoice to a pdf and email it. All pdf's are named "Customer Last Name" Invoice "Date" e.g. Davis Invoice 042814, and saved into my Dropbox folder. It makes them really easy to access and search from my phone.
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