I used to use MacFreelancer and I wasn't at all happy with it... had a few strange quicks and it was hard looking up things by invoice No.
I moved over to Freshbooks at the beginning of last year and have been incredibly happy with the service. They have great customer service and are proudly Canadian, so I was happy to keep my dollares in the country
You have to consider your personal workflow. Are you always on the road? Managing multiple computers / devices? Working away from your computer?
I'm maybe a little old fashioned and like a dedicated desktop application, so I use Billings. But if you're not in front of your main computer when you're working, you might want to consider a web-based invoicing app. There are lots of them out there.
As an aside, the iPhone Billings app is interesting, but definitely not slick. It requires manual intervention to sync the data. But the desktop app is pretty good (but could be a whole lot better). And they're a local GTA firm, if that matters to you.
Because I do small scale hosting for some of my clients, I had set up WHMCS (WHMCS - The Complete Client Management, Billing & Support Solution) for automated hosting billing. Then I started using it for other design work and stuck with it. It is flexible enough to allow me to use it as a CRM and create invoices for clients. Because it's online, it also allows my clients to log in and modify their details, make online payments, view invoices, etc. It automatically sends reminder emails when they are late, automatically charges late fees (if I so choose) and has great stats and reports (for tax purposes). I can even create invoices in advance, add my time as I go, then on a specified date it invoices them automatically for all the work to date.
Not for the faint of heart as it requires you to have a fully self managed web server (or at least a VPS) but I'm glad I got it working.