I know a lot of people hate the buttery flavor of shipyard's yeast, but I am a fan of it for certain styles, especially pumpkin beer. Do they bottle condition any of their beers? I ask for harvesting purposes.
No, to the best of my knowledge nothing from them is bottle conditioned but the ringwood yeast that is used should be able to be harvested since they are not pasteurized. Try is out and let us know.
Any tips on taking yeast from an unpasteurized but not bottle-conditioned bottle? There will be less of it, since it's filtered and force-carbonated.
No real need to harvest from a bottle, you can simply buy the yeast. Unlike 'bugs' from sour beers. Wyeast and White Labs cultivate and grow nearly all the commercial yeast out there and there are charts to figure out the origon of the yeast. If you want to mimic Shipyard (gag), simply brew warm and the second fermentation is done: package it. That'll insure the yeast has zero time to clean up any off flavors such as diacetyl. There was a blog floating around about an employee of Shipyards expierence there. Interesting read. Crappy brewery.
This is only slightly off-topic: anyone else see that Shipyard announced they are releasing bourbon barrel aged beers, starting with BBA Double Old Thumper? http://shipyardbrewing.blogspot.com/2012/02/bourbon-barrel-aged-brews-coming-soon.html
No need to harvest yeast from the bottle. It's not secret they use the Ringwood strain, which, as mentioned, you can buy quite easily. However, if you wanted to harvest it just for the hell of it, Blue Fin Stout is not filtered, so I would start there.