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.
I have been looking through articles on your website and found them very helpful. My husband and I just began our own nonprofit a few months ago. I could not agree more that the software chosen is crucial. We have a friend that I also work for who developed a software with many individuals, like me, in mind. The software is made for individuals with little or no accounting experience that does not present with an intimidation factor. While simple to use, it still handles accounting needs. Anyone interested can check it out http://www.aplossoftware.com – thanks again.