I use toggl for timetracking, and am currently investigating bullet and xero for accounting/invoicing. Can't recommend one over the other just yet, but preliminary thoughts are that bullet would be better if you don't currently have an accountant, whereas xero is a tool to empower your accountant.

I use Harvest for the retainer feature

Ballpark has an app for iPhone and handles invoicing as well!

I use Hours Keeper as my preferred app after using Harvest, it's simple and clean. Plus, I can easily export the .CSV to Harvest to bill. I switched because, I had a little more options but simple functionality while being completely free.

Klok — not the prettiest, not "flat", but it's a cheap one-time cost and works well.

I use On The Job. Probably not the best looking one. But it works like a charm!

Timely

I've been happily using FreeAgent for years. It's great. You can get 10% off with this link: http://fre.ag/41kxz40y