I use Cushionapp to estimate, track, and invoice my clients. It has a handy invoice feature that will send a nice looking invoice straight to their email. It's also integrated with stripe so that I could accept payments for an invoice right on the web. About half of my clients pay that way, the other half pay use wire transfer straight to my bank account. I include banking information with every invoice to make things easy.

In the past I've Billed every two weeks or twice monthly, but I've switched to weekly billing and it's improved client responses and payments a lot!

some friends use invoiceplane. Other use ninjainvoice.

i use billyapp, but now using the accounting software provided by my bank (helps with taxes, i am told)

Zipbooks - has time and project based invoicing, reminders, payment integration and simple to use