Luckily, we were not hit with a penalty but we are supposed to estimate b/c we paid over $2000 in taxes for the 2006 tax year (yes, don't ask, capital gains). We decided to not estimate for this year as we are not selling any stock in 2008 and should actually get a refund or come close to zero. We actually didn't "sell" any stock but some stock my DH owned was called in with a sale of a company. So the stock sold, we got cash and a huge capital gains on which we had to pay tax.
We also upped our withholding since we hadn't done that in years.
I know my reply doesn't relate to self-employed but I agree that estimating taxes quarterly is a good idea if you know you will have a larger tax bill in April. However, since the stock sold in December, we couldn't really estimate throughout the year--our financial advisor actually was surprised it was called in at all since companies were merging and she thought we would just be issued shares of the stock in the new company. (Phone utility). We just took a hit and had to pay for it.