Mr. Ected said:
I am in the middle of a refi also. My lender was looking at house values on Zillow.com (He said he usually gets a fair estimate) and the appraisal came in $40k under the Zillow estimate. The PITA was the fact that with the estimate we could have easily walked in and out without putting out a dime, now with the lower appraisal, we will have to shell out ~$6k in order to not have PMI on the loan.
Was talking to my lender about this whole thing, and I jokingly said that wouldn't it be nice if we could just go to the appraiser and say "Can't you just give us $10k more?" He came back with that in the past they could, and that is partially what lead to the Housing Crisis people were mentioning above. Since 2007, the lender isn't allowed any contact with the appraiser, there is a dept in their bank (SunTrust) that deals with them solely. Now I understand that $10k on my place isn't going to cause the world to end, but you can see how lenders saying to appraisers, "give me X on this house or you won't work for me again" and the X being large, could lead to bad things.
In the end, since we are not financing what amounts to the closing costs, we will actually save more per month on the new loan, and with a skipped payment with the timing of the old and new loans, we will make up the amount we shelled out in about 6 months, so it will not be a big deal.