[Number of dragon limbs?]
Two. The forelimbs are the wings.
[Are dragons male, female, hermaphroditic, or is there something magical involved in their reproduction?]
Sexing dragons is difficult. More in future books.
[Do all the Great Houses own Valyrian steel weapons?]
Oh, there are more Valyrian swords than we have seen so far. Not all of them belong to the Great Houses. Lesser nobility would oft purchase one as well, for the prestige, and sometimes knights or even lesser swords would acquire one on the battlefield, after the original owner fell. But there have been no more made since the Doom of Valyria.
[Can a maester's chain include multiple links of the same metal?]
Mulitple links are possible, and signify that the maester is especially accomplished in that area.