Depending on your profession, you may need to track the time you spend on each client or project by the minute. One lawyer I know recommends keeping a client hour tracking file open on your desktop always and having it minimized when you are not logging your time in it. If you have an electronic file open like this on a daily basis, it makes it much easier to fill out your time card, log client billing hours, or maintain any other system you might need to make your record keeping much easier. Check out On The Job, stuntsoftware.com/onthejob, it comes highly recommended, seems super easy, and is extremely accurate.
If you are just starting out, a free- yes free- online service to consider is: BillingBoss.com. It has great features such as allowing you to accept credit card payments and manage your account with a smart-phone. This is an excellent option for people who often travel and are comfortable using their smartphone on the go.
Aside from QuickBooks, there are other accounting and invoicing programs out there to consider as well. freshbooks.com is a much simpler way to do online invoicing and yet it has other features such as invoicing in foreign currencies and scheduling recurring billing that might make this a great solution for your business.