Intuit's QuickBooks Pro is an absolutely essential software program for anyone running a business. It's especially important for people running an online business, such as an eBay business or an ecommerce site.
I found QuickBooks a little daunting at first. But when I kept at it, I discovered it was easy to use. If you're running an eBay business, you just enter your sales as sales receipts. Then PayPal, your business checking and other accounts are tracked as bank accounts. You track your credit card account as well, and QuickBooks does all the accounting behind the scenes. It helps greatly with taxes, and integrates well with TurboTax.
QuickBooks integrates well with other software programs. I use it with eBay's Accounting Assistant, which downloads my eBay transactions and PayPal transactions, including fees, for me with little effort on my part. I strongly recommend that you use this software if you run an online business.