Freshbooks (Recommended by respondents)
QuickBooks (Recommended by respondents although it may be overkill if you are using for just invoices)
PayPal
PaySimple
Zoho
LessAccounting
Blinksale
SimplyInvoices
Cashboard
SimplyBill
InvoicePlace
Google Apps Wave Accounting Package
http://www.invoicejournal.com/
http://freelanceswitch.com/money/7-online-invoicing-apps-for-freelancers/ (Ranks the different invoice apps most of which are mentioned above)