While this is not an official endorsement, I use QuickBooks Pro to keep my books.  It's simple and easy to use.  The main reason I chose QuickBooks, was that my accountant recommended it, and uses it.  Every so often I give a backup to my accountant and they review my books.  I found out that Intuit has a great accountant's program, where for a few hundred bucks they can get several special copies as well as other benefits.

With that said, I would actually prefer they use Microsoft's Accounting program.  The main reason being, it's free for me!  I get it as part of the Microsoft Partner Program (http://partner.microsoft.com).  But, since my accountant doesn't use it, it would be foolhardy for me to switch to it.  I did find out a tidbit of information that I am going to try and get my accountant to do.  Accountants actually qualify for the Microsoft Partner Program.  Don't ask me how, I don't know. 

In fact, how I found out about it was through some complaints to the Redmond magazine.  Evidently some partners are ticked because they are losing revenue since accountants can sign up for the $300 Action Pack and get the accounting program, crm software, office, and operating system licenses.  Since I don't sell those services to my accountant, their tech support vendor doesn't as well, and since they buy all their products from off he shelf, I'm going to get my accountant to sign up.

So, before you get your accountant to sign up, please make sure you're not affecting someone else's bottom line.  I never recommend making enemies.  Especially when it would only save you $200, the cost of QuickBooks Pro.