My GF is an accounting major, she wanted to chip in, so here she goes. She is kinda opinionated...fair warning!
I've used Quick Books (all versions) since 1996 in two business scenarios. Both businesses did have, at times, close to 100 employees each. The payroll function within Quick Books is excellent. My W-2's were always flawless and I was able to provide the accountant copy within the program at year-end to our CPA firm. He never had any problems with our numbers.
The major misgiving in Quickbooks is Inventory Management. I would not suggest Quickbooks for a parts manufacturer requiring JIT or other programs to manage 500+ parts in inventory. You will just want to kill yourself.
However, if you are running a basic organization with salaried and hourly employees, providing services and/or products, with a general A/P and A/R setup then Quick Books is for you. There are two potential pitfalls, however, with any accounting software that you must avoid in order for your books to balance.
a) If you have an existing business account, you must "backload" and reconcile all checking account data within Quickbooks BEFORE you begin entering new transactions. If you do not, your reconciliation feature will never work right and your Accountant will hate your guts. Trust me, I physically witnessed this and it took two years to fix three tax years - do not try this at home!
b) Before you enter any data at all, you must set up and define your chart of accounts. Check with a local accounting firm if you do not have any accounting experience to get a crash course, what accounts to include and what each account should contain, and be scrupulous when entering data. Reclassifying data at tax time is costly and time consuming. NEVER use accounts such as Other or Miscellaneous -- your CPA will not accept entries to these ledger accounts and you will be audited.
c) In order for many of the reporting areas to function well you must load your budget into the program. Otherwise, your budget versus actual reporting will not work.
d) Be very careful about how you classify Other Income. For instance, if you receive rebate income non-tax (because someone else already paid the sales tax) verify that the tax code is set up to reflect non-tax and that you state it as Non-Taxable Other Income on your Income Statement. Quick Books assumes everything is taxable unless you tell the program otherwise.