Accounting isn't fun to most people. Volunteers that do this are typically very detail oriented and organized. If you can get an accounting firm to do your books as a pro bono that is great. If you are a 501(c)(3) non-profit, it is also ideal to get a CPA or accountant on your Board of Directors.
Quickbooks and Peachtree are probably the most common accounting software packages out there. Once you use one, you will be married to it for life, because it is difficult to transfer data to the other. If you are a 501(c)(3) non-profit, you can sometimes find Quickbooks cheaply on TechSoup.
Salesforce.com has a charitable Foundation that provides 10 complimentary licenses of Salesforce.com's CRM tool to qualifying non-profit organizations to help them manage their donors, volunteers, partners, marketing campaigns, donations etc. The complimentary licenses are valued at about $ 14,400 per year.
Point of Sale
Who uses what?
We use Quickbooks and Quickbooks POS, and instantly share the data files to various board members using Dropbox. Relative to other products, it seemed to be FAR cheaper, but they seem to get you in any customization with auto-renewing monthly support contracts. Not to mention if you want to accept credit cards, the POS software makes it impossible to use any other credit card processor than, you guessed it -- Intuit. The rates aren't good or bad, but it would be nice to have other options.
All donations, new parts sales (taxed), and used parts sales (not taxed) are run through the POS. The Shop Manager then closes out the till at the end of the night and the amount is checked and deposited.
Online donations are accepted through Google Checkout, which charges 0% (free) as long as you are a non-profit part of the Google Grants program.