Depends.
If you need something cloud based, that doesn't market itself to your customers, that's free or affordable, I would check out paydirt.com.
If you want something self hosted, the one that really impressed me was Pancake. Built on CodeIgniter and PHP, it's pretty powerful, and getting better. Even offers a secure client area. Email set up, in my experience has been quirky, but that's been my only realy complaint with it. The support is good, the invoices and proposals it creates are passable, and it even tracks how much money you're pulling in. Good stuff. http://www.pancakeapp.com
