After a bit more than six months freelancing, I've started to hone in on the systems + web apps that help me stay the most organized. To me, organization is one of the most crucial elements of life, but that could just be my Virgo tendencies speaking. :)
Time Tracking + Invoicing
I very recently made the move over to Harvest for my time tracking + invoicing. This web application has time tracking and invoicing capabilities, allows PayPal Business Payments (which means I only pay a $0.50 flat fee to PayPal every time I get paid!), and automatically sends a thank you email after an invoice has been paid, as well as automatically sending a follow-up email if a client does not pay their invoice on time. It's also more affordable than FreshBooks, if I was to upgrade to a paid plan, at only $12/month as opposed to $19.95/month. I know that $5.95 a month doesn't seem like a big difference, but believe me.
I use Google Docs for pretty much everything else that I do. I have spreadsheets for statistics + finances, have client folders + docs. I love it because I can do my work from any location and know that all of my information is safe and secure. I run my email accounts for Spikes and Stardust through Gmail, which allows me to have access to everything on the go.