Intuit – you know, the folks who make QuickBooks – have put together an online invoice-management site called Billing Manager. You enter your company information, and your client information, and what invoices you want to send with line-item detail, and it takes care of a lot of the donkey-work. That includes emailing nicely-formatted invoices, tracking everything for you, sending reminders, and letting you tag address-book contacts into groups.
Billing Manager is free, and though you might think it would integrate with QuickBooks, it doesn’t seem to. It does allow you to sign up with the QuickBooks Merchant Service to accept credit card payments (and that, of course, is a pay service). For more full-featured solutions, at a price, you may want to look at the competition like FreshBooks or CashBoard.