Hi, I did something really dumb-- I inadvertently applied 5v of supply to the 3.3v pin. Smoke ensued and I quickly disconnected. I believe the smoke might have been coming from the 5-pin component labeled "LFPG" right above the Atmel DIP package. I'm not sure what component this is and wasn't able to decipher the schematic.
The board still works. After the smoke, I powered it up via USB and reprogrammed it. However I surely damaged something and would like to replace whatever it was to avoid any future surprises with new projects.
The poor thing was probably frantically trying to get the output voltage back to 3.3v, which wasn't gonna happen as long as +5 was connected to it.
Check that it's still outputting 3.3v, and that both USB and external power work correctly (and give you 3.3v where it should).
Assuming no problems are found, I'd count myself lucky and put it back into service.
Smoke does not always mean a part has died - sometimes the smoke is coming from left-over flux, or the substrate around a trace or part that's getting way-too-hot, and you can save it if you disconnect it in time.
As stated measure the 3.3v out... you can buy 10 of those LDO 3.3v for a couple of bucks free postage on ebay. All you need is a soldering iron and a bit of patients.
A word about smoked chips that appear to work. I accidentally plugged a 10 v. signal into an A0 pin on a ProMini for just a moment. The ProMini went bonkers, but went back to working right after I reset it. About 48 hours later, the A0 pin gave up the ghost (developed internal short). So at the very least, if you think you've stressed a chip, you probably have. I was only a few hours away from soldering that ProMini down to a PCB; so my lesson is, never use a chip that you've stressed, but appears to be working, where it is meant to be critical or permanent.