I've been a big fan of Freshbooks and have used the invoicing system and time tracking tool very easy to use. It's built in tools to help you collect overdue invoices is wonderful. What I didn't like about it is it limited th number of clients I could have (the more clients I had, the more I would have to pay).
I hated that the third party app that I used to track time on my desktop quit working.
I hated that when I paid them, my money had to go through a conversation and as the US economoy is crap, I always got the short end of the stick.
Then I stumbled across Harvest.
It's $7 less a month for their smallest account, and it has UNLIMITED Clients, UNLIMITED Projects, and UNLIMITED invoicing. They have all the basic tools you need, and the ability to tie in with a TON of third party apps. You can track time on your iPhone, Droid, iPad, etc. It does all the “nudging” and collections that Freshbooks did, AND it has a retainer tool (very cool).
I was playing with the system and (for lack of a better phrase) tried to make it do something stupid. The system wouldn't let me. However, I didn't know what I was doing was being “silly.” I sent an email to their support and got a very quick response. That made my decision to move my billing to their system a “no brainer.”
If you're interested, check them out at getharvest.com
[soundcloud url=”http://api.soundcloud.com/tracks/50487981″ iframe=”true” /]