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QuickBooks or QuickBooks pro is a good one. If you use one of those your Accountant (if you use one) can usually import your data to do your payroll taxes and corporate stuff. They may even give you a discount because you can e-mail them your stuff. And QuickBooks pro has good telephone support, I think that a good CPA firm or Accounting firm should do your major stuff but if you are a small shop with a couple of employees QuickBooks pro could do everything from Invoice to Payroll and even figure the payroll tax deposits so you are never late.. (you don’t want those late fees) The billing portion will also keep track of your sales tax so you send that in also. You don't want a sales tax audit they suck!
Sorry I rambled on. My father is a CPA here locally and I hear horror stories about businesses that do not have the books in order. The IRS can be a bear! I am glad that his office does my stuff!
Quickbooks baby! I hate doing paperwork, and I barely sneak along with Quickbooks, but it's lightyears ahead of anything else I've seen. Comcash is the only other one I've fiddled with really, and that was a living nightmare.
I just signed up for their "assisted payroll" services last month since I bacame an LLC & need to pay meyself through a proper payroll structure for the first time. I'm also very happy with the opportunity to have their help getting all the complex tax filing done for me in a timely manner.
JM is right, talk to your accountant before you invest in software.
While QuickBooks may be a popular program, if your accountant doesn't use it, you may be asking for trouble (trouble = $$ out of your pocket).
I use a combination of EstiMate Software and QuickBooks. Both are well worth the investment for me.