MetaChat is an informal place for MeFites to touch base and post, discuss and
chatter about topics that may not belong on MetaFilter. Questions? Check the FAQ. Please note: This is important.
Seriously, I had my current house appraised, too, and it was way under my expectations. I figure that I'm still going to buy the new one, but might as well try to get a better price.
All things considered, I'm lucky that I'm going to be able to live in a cute house with a great view, but it's real money, and I'm a wreck.
The seller chose not to re-list, after previous listings expired, and at least 1 buyer bailed at the last minute. Once I found it, bringing in a real estate agent didn't make sense. I wasn't looking hard, but this house just fit.
I would offer slightly (2-3k) over appraisal, if I was comfortable paying it--basically whatever it was worth to me to close the deal. Closing on something you love may well be worth paying a small premium over appraisal. Also, don't be afraid of the negotiation. We had three or four counteroffers over small things (the cost of the electrician for one) when I closed on my place. It didn't kill any deal and I was not the only interested buyer.
I would offer a small premium over appraised, especially if I wasn't planning to turn around and sell any time soon. Because you dropped costs on appraisal and the like, I would expect the seller to cover all closing costs. They usually do anyway.