When using an estimator, so long as the net profit from your S corporation is added to your total income as ordinary income (and not subject to any additional tax other than income tax) the result will be correct.
Qualified dividends and capital gain income (and perhaps even other investment income) have special tax rates and are not taxed at your marginal tax rate for ordinary income. That is, qualified dividends are taxed in 2010 at 15% rate regardless of the amount of your income.
For example. at http://turbotax.intuit.com/tax-tools/calculators/taxcaster/ your S corporation net profit could be entered as miscellaneous income but could not be entered as dividend income or gain/losses. The tax rate on ordinary income is progressive and increases (10%, 15%, 25%, etc.) as total income increases. The tax rate on qualified dividends is always just 15%.
You could even add the net profit to your wages and get a correct total of income that will be taxed at the proper rate since wages are ordinary income and not subject to additional taxes.
You do not want to list your net profit as business income as that type of income is subject to self-employment tax and your S corporation income is not (unless you have decided it will be treated as if it is, due to not paying yourself a wage).
Some calculators will have a category, or line entry, for income from S corporations (and rentals, etc. on Schedule E). For example see the 1040 Tax calculator at Taxes & Payroll
I hope this helps clarify that you want to choose any income category that will have progressive rates and not be subject to self employment tax when entering the S corporation net profit in a tax estimator.