Blizzard's new Dungeon System (with built-in cross-server LFG) coming in patch 3.3 seems to have all of its bases covered, even tiny niggling details that are not yet covered in the patch notes, as this post by Zarhym proves.
What happens with Stone Keeper's Shards when you're in a PUG that takes advantage of cross-server LFG? Well, that's easy, kiddo. The system will check to see if your home realm's Wintergrasp is captured by your faction. If it is, voila! Stone Keeper's Shards for you. If not, well, you can figure it out.
As for everyone else in the group, the same check is made, and if someone else doesn't have WG captured on their server and you do, they won't even see the Shards on the corpse, so no "Hey, what about MY shards?!" loot confusion should come up. If it does, well, you'll probably never see that person again anyway, so say what you must! Just bear in mind that parties in patch 3.3 do have that new Vote Kick option.
Patch 3.3 is the last major patch of Wrath of the Lich King. With the new Icecrown Citadel 5-man dungeons and 10/25-man raid arriving soon, patch 3.3 will deal the final blow to the Arthas. WoW.com's Guide to Patch 3.3 will keep you updated with all the latest patch news.