I own 2 companies in Texas, company A is a LLC and company B is a
Corporation.  Both companies were created mid-2000.  Company A made
around $500 or so in 2000, and company B has never made any money.  I
have never filed federal income tax returns for either company. 
First, what forms do I need to fill out, and what fees/penalties will
I have to pay?  Second, is there any tax software that can automate
filling out the forms?

Dear JThoma1,

Catching up sounds like fun. But it won't be so bad.

You can get software from TurboTax for about $100 for each year
http://www.shop.intuit.com/store/jhtml/past_year.jhtml?productLine=2001&priorityCode=5030201
(At that price, I'd look for a good local tax pro instead.)

The good thing is that you are in Texas...and they
don't have state taxes. Just forms....
http://www.window.state.tx.us/taxinfo/taxforms/05-forms.html

For Texas, you will need to complete these forms for 
both the LLC and the corporation:
Form 05-142 Franchise Tax Report
http://www.window.state.tx.us/taxinfo/taxforms/05-142.pdf
Prepare one for each year.

Form 05-142 - Public Information Report
2002 http://www.window.state.tx.us/taxinfo/taxforms/05-102.pdf

The other good thing is that with little or no income, 
you won't have much to pay in taxes. If anything.

For the Corporation, you will need Form 1120
2002 http://www.irs.gov/pub/irs-pdf/f1120s.pdf
2001 http://www.irs.gov/pub/irs-01/f1120.pdf
2000 http://www.irs.gov/pub/irs-00/f1120.pdf

Unless you are an S-Corporation, in which case, use Form 1120S
2002 http://www.irs.gov/pub/irs-pdf/f1120s.pdf
2001 http://www.irs.gov/pub/irs-01/f1120s.pdf
2000 http://www.irs.gov/pub/irs-00/f1120s.pdf

For the LLC, you have three choices:

You may use either the corporation form - Form 1120 (See above)

Or you may use the Partnership Form, Form 1065
2002 http://www.irs.gov/pub/irs-pdf/f1065.pdf
2001 http://www.irs.gov/pub/irs-01/f1065.pdf
2000 http://www.irs.gov/pub/irs-00/f1065.pdf

Or you may include it on your personal tax return on Schedule C.
2002 - http://www.irs.gov/pub/irs-pdf/f1040sc.pdf
2000 - http://www.irs.gov/pub/irs-00/f1040sc.pdf

If you have an S-Corporation, use the partnership form, or
Schedule C, you may need to amend you personal tax return
for those years. The income or loss passes through to 
your personal tax return. But that's a whole other discussion.

Incidentally, just because you had $500 in income for your
corporation doesn't mean that's your profit. Remember to 
deduct your costs of operation (including auto expenses). 
To amortise the costs of incorporating over 5 years. 
And to depreciate any equipement you may have bought.

Have fun!

Your TaxMama-ga

Thanks taxmama!  Great answer as expected on Google Answers!  I think
I will try to find discounted versions of Turbotax Business and just
print out the returns and mail them in.