It depends on the organization. QuickBooks Pro works well enough but may not be for everybody. The article from Idealware gives a pretty good round up of the type of packages out there at various price points and the pros and cons of each.
Another nice piece on selecting accounting software from a GuideStar Newsletter article by Nancy Church. No new or different brands of software listed but lots of good questions to consider.
From the Nonprofits Assistance Fund comes this nice piece about questions to ask and things to watch out for when choosing a new nonprofit accounting system.
The AICPA’s Journal of Accountancy recently had an article comparing different nonprofit accounting software packages. It is not a complete list but it is one of the broadest evaluations of current offerings I have seen in some time.