With Pancake it's also a one time fee only. Much cheaper in the long run, fresh books is to expensive for what it is. For Pancake, you can also write or buy your own custom theme to keep look and feel. (I'll be starting a theme site soon, with themes <$5).
pancake. Very interesting. You've been using this for a while?
Yeah, I'm migrating away from FreshBooks. I really like Pancake.
Got some really great features too, like automatic file delivery upon payment.
A friend of mine is the lead developer on it. Pancake grew out of a need for a better invoicing system. Fresh Books is good, but it's to expensive for what it offers. And it was missing a few key things for us.
As a group friends & small business owners we wanted a different option. After searching and talking to others we found out lots of other people did too. So my friend decided to build one. It launched about six months ago, and has been really well received. It's gaining momentum now and is doing well. I recommend it to people because it's great, affordable, and it works.
One of these days I'll get around to the themes site. I should probably do that sooner than later.
As it's self hosted so you don't have to worry about server security (just your own), or it being the subject of a large scale attack - the same way you would with FreshBooks for example.
All money transactions are done via paypal, and tied together using their API.
As for the login, it uses a combination of sha1 with a salt, which is pretty solid. If you were really paranoid - since it's self hosted - you could further protect the admin directory with an .htaccess, but I'd think that overkill.
Does that answer your question? Or were you wondering about something more specific?