Hello !
I was working for an employer till May.  Then I had a sole prop
business (consulting) till Aug.  Then I started an S corp (consulting
company) in Aug and I worked for that S corp.  I did not receive any
salary from the S corp.
Come tax time this year, I was not able to find time to file the
return.  So I decided to file for an extension.
I calculated my approx tax liability by including my salary, my sole
prop income and the s corp income.  Then I filed ONE extension along
with the estimated tax payment.
I did not realize that I should have filed a separate extension for the S corp.

What should I do now?  What forms does one need to file for an S corp
return?  What extra forms do I need to file due to failure to file? 
How much will the penalty for late filing be?  How do they calculate
that?  Can I request a waiver of the penalty?

The S corp has no employees but me.

Dear GTG,

Well, there's good news, at least on the IRS front. 
Since S-Corps do not pay federal income tax, you will have
no penalties or interest for filing late. 

The information you'll need to know about filing for corporations
is in IRS Publication 542 (2003), Corporations 
http://www.irs.gov/publications/p542/index.html

The publication includes samples of the 1120 returns
http://www.irs.gov/publications/p542/ar02.html#d0e3465

One note though, you'll be filing similar a form - the 1120S
http://www.irs.gov/pub/irs-pdf/f1120s.pdf

Specific instructions for the 1120S can be found here
http://www.irs.gov/pub/irs-pdf/i1120s.pdf

The instructions will explain what other forms you'll need,
which may include Form 4562 for depreciation, Schedule(s) K-1
for yourself and any other shareholders. 

You'll find links to all other forms here. 
http://www.irs.gov/formspubs/lists/0,,id=97817,00.html

You will need to prepare the S-Corp return before you do 
your personal tax return. The income or loss from the K-1 
will be a part of your own Form 1040. Report it on Schedule E,
page 2.

Now, the bad news, maybe. You don't say what state you're in.
But some states, like California, do charge a tax on their 
S-Corps. So, you will have late filing penalties if you're in
one of those states. To find the forms and information for your
own state, please use this link - it will take you to a map of the
US. Just click on your state. 
http://www.taxadmin.org/fta/link/forms.html

Some good advice, though? Don't prepare this return yourself. 
Particualarly in the first year. Go to a good, local tax professional. 
There are some issues you're ignoring besides missing the filing
deadline. A big issue with IRS these days is owner-employee wages. 
You must discuss with someone in your community who understands
more of the current issues with IRS and your state. 

This should get you started in the right direction. 

Oh, and remember for next year - Corporate returns are due on 
Mar 15th (if your year ends on December 31st). So if you're not
ready, that's when you file the corporate extension. 

Best wishes, 

Your TaxMama-ga