I can't speak for Latvia or Estonia. Lithuania is in the "relatively" fortunate position of not having a large ethnic Russian population. (Some say because of the anti-Soviet guerrilla-movement that finally gave-out in the early 60s). But there is a fairly large Russian population in the capital city, Vilnius. For the most part everyone gets along, possibly because the Russians understand that their standard-of-living would decrease if they returned to Russia. (For this reason, many ethnic Russians were actually pro-Lithuanian independence).
Furthermore, since Lithuania is a parliamentary democracy, the ethnic Russians have their, albeit weak, representatives in government. As a side-note, there is also a small and vocal Polish minority agitating for school to be taught in Polish. (Shades of the bi-lingual education debate going on here.) Incidentally, most Lithuanians speak Russian, and vice versa. It's good for business.
But there is friction, occasionally, since most Lithuanians bristle at the thought of the occupation and the damage it caused, and tend to view the Russians as interlopers. For their part, the Russians are resentful of their relegation to "second-class" status. A personal anecdote: while standing in line at the Klaipeda post-office (a port city also with a large population of ethnic Russians), an old man "shouldered" past me to the front. (A direct result of the Soviet days--most Lithuanians and Russians don't tolerate lines). When challenged, he indignantly responded (in Lithuanian), "You youngsters have no respect for the elderly . . . I am a decorated veteran of the Great War."
I was going to let him pass (he was old, after all), but my Lithuanian escort responded, "Shut up, old man, that is no longer considered to be a privilege here." I kept my mouth shut, realizing that a principle was at stake. The comment was well-received by maybe 50% of the 10 or so people in the lobby. The old man backed-down, and nothing happened. But in a nutshell, the episode demonstrates how "complicated" things can get.
As for Nazi recidivism, there is none to speak of in Lithuania. However, because of the general reluctance of the Lithuanian government to prosecute Nazi war-criminals (one case was recently dismissed due to the defendant's poor health), and its insistence on prosecuting pro-Soviet collaborators (witness Mikhail Gorbachev's outstanding arrest-warrant), certain commentators in the U.S. perceive that "double-standard" to be a tacit acceptance of anti-Semitism. And wouldn't you, if you were a commie-apologist? Clearly, axes are still grinding on both sides.
Last anecdote: my last visit to Lithuania coincided with a visit by Sen. Tom Lantos (D-CA). While participating in some sort of a forum he launched into a table-pounding tirade concerning the Lithuanian government's refusal to prosecute the above-mentioned Nazi. The eyebrow-raising, near-universal, Lithuanian reaction was: What a jerk. After most members of his Party coddled a succession of Soviet dictators, excused their lies, treated Gorbo like some sort of a friggin' hero, and turned a blind-eye to his human-rights violations, this guest of ours presumes to lecture us about the allocation of justice. Lithuanians have a long memory.
I'd have figured they'd have gotten over Gorby by now, what with his overseeing the dissolution of the USSR and all.
C'est la vie, I guess.