This article is long (I'll admit, though I've had it up in browser a couple days I've still only read half of it) but it's a really fascinating survey of current research into where the Japanese people came from, both historically and linguistically. This is an unusually charged question, as linguistic and archeological questions go, because a great deal of Japanese (and Korean) national self-identity is caught up in the question. And evidence is intriguingly sparse and contradictory. (For instance, linguistics would suggest that the Japanese language split off from Korean -- it's apparent closest cousin linguistically -- at least 4,000 years ago, yet genetically Japanese are very similar to mainlanders, suggesting a fairly recent divergence.)
On a slightly related side-note, one of the things that's always struck me watching Japanese anime is that there seems to be a cultural perception in Japan that Japanese are "the white people of Asia". Japanese characters often look, to American eyes, very nearly European or American, while Korean or Chinese characters have very strongly Asian features. There also seems to be a real fascination with settings (more often fantastic than historical) which are clearly patterned on or explicitly set in turn of the century Europe -- though often Japanese names are mixed in freely with vaguelly Germanic ones.