This is not intended as a full accounting and bookkeeping check list.  In fact, it's specifically designed for non accountants.

• Check for and account entitled "Opening Balance Equity".  It should not be there.  If present investigate entries and reclassify. 
• Check your chart of accounts for any inadvertent changes.  Often times you'll find two accounts for one thing.  For example, "Auto "Excise Tax" and "Excise Tax" 
• If you use "items" in QuickBooks review the item list and connection to your chart of accounts.  If the connection isn't accurate your reports won't be either.
• Check the "Retained Earnings" account.  It should be the same as on your finalized tax return and financial statements from last year.  The best defense to errors here is to lock your accounting period once year end work is complete.
• Check for open purchase orders and sales estimates.  Confirm that the outstanding ones reflect orders still in process.   Delete old outstanding PO's and estimates as they clutter your files. 
• Confirm that your backup procedures are being followed.  Consider automatic backup online through QuickBooks or at the very least, automatic backups each day.  If data is destroyed and you forget who owes you money - it's just like throwing money away.
• Check the outstanding items on your bank reconciliation.  It's not unusual for old transactions that will never clear to remain.  Take care how you void any outstanding items from a closed period.
• Review your aged accounts receivable listing.  Stay on top of your customer balances.  Don't let open invoices go beyond 30 days.  Note if customers are paying current invoices and letting one or two just sit and age.  This could indicate a problem invoice. 
• Check your aged accounts payable report.  Old bills that won't ever get paid cause problems with your financial analysis.
• Finally, read your general ledger report.  This is a great way to find misclassifications or other errors.

You don't have to be a CPA to review your books.  But don't misunderstand, this list just scratches the surface.  You'll want periodic reviews by a trained CPA to address the many other issues that must be considered.

We're able to connect online to our clients files using a web site called gotomypc.com  We can review our clients files from our office, thus making interim review efficient and less costly. 

More than that, when our clients have questions we can "drill down" directly into the problem.  We can then find an easy solution to the problem rather than spending wasted time just trying to describe the problem.