Harvest. It has nice time tracking and billing based automatically on time (or independent of time if you want). Plays nice with a bunch of GTD apps like Basecamp and Trello. Decent phone app, too. I looked at Freshbooks and Quickbooks online before I settled on Harvest a couple years ago. If you use this referral we'll both save cash: You have been invited to try Harvest.
I've been using AccountEdge Basic since July. I'm currently looking into cloud based options. AccountEdge Basic is good...but it's a little complicated for my current needs. It might be perfect for you though...or might not....it's a good program is what I'm saying. I'm just wanting to find a really user friendly invoicing, accounting, inventory tracking program that isn't filled with accounting jargon. A friend of mine was telling me the other day to look into FreshBooks. I think I'm going to give the free trial a shot and see if it'll work for me.