^I always just assumed The Others took them to get DNA samples,
Me too. But I don't think most of the audience would get the connection between the luggage tags and the hair in the brushes having DNA, so that it's easy to match up the samples with the owners and no one's the wiser. So they should explain it. Even having the brushes discovered in a lab, in containers labeled with everyone's names would be enough.
What the hell was with the vaccines that Desmond and Kelvin were taking religiously?
Might have been a cover story, but I've wondered whether it was a mis-interpretation of the "disease" that Danielle was worried about - if they thought that the disease was communicable instead of caused by being resurrected as a Smokey-controlled demon (or whatever), then maybe the vaccines and the suits were a precaution against it?
As for the polar bears, isn't there something about the island that raises animal intelligence (though it sometimes has the opposite effect on humans

) and Dharma wanted to see how smart the polar bears would get?
As for "why polar bears," well, why not? If you're going to test various species to see how the island affects them, gotta start somewhere.
But Tunisia reminds me - why does the island teleportation link go to Tunisia of all places? Is it "natural" or was it engineered that way for some reason? Is that how all the ancient Egyptian stuff got to the island (someone blundered across it thousands of years ago?) Are there other teleportation destinations and the teleporter just happens to be aligned with Tunisia and nobody knows how to change it?
And what about that scene with the Antarctic researchers - what do they have to do with anything (if that was explained, I've totally forgotten.)