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Perhaps you should have read through to the end some of the websites you posted:
http://news.yahoo.com/s/afp/20061203/ts_afp/britainrussiaspy
"The Observer newspaper said the US Federal Bureau of Investigation had accompanied Scotland Yard detectives during questioning of another Russian exile, former KGB agent Yuri Shvets, in Washington.
Shvets -- who has links to London-based dissident Russian tycoon Boris Berezovsky -- reportedly compiled a file Litvinenko had in his possession containing potentially damaging revelations about Moscow and the state takeover of Russian oil company Yukos."
So yes, Yukos is involved in the case now, specifically Putin's shady maneuvering to strip its executives of power and secure for the Kremlin majority ownership.
Don't get me wrong, I have absolutely no love for Russia's robber-barons either. But as the post below noted, the only difference between Putin and one of Russia's countless billionaire tycoons is the power-base each was able to consolidate around him. An executive at Yukos had wealth, connections in the business world, and the leverage that comes from controlling a small chunk of an inelastic resource like oil. Putin had the "legitimate" powers of the state - the police, the security services, and the provincial governors. It just so happened Putin knew how to wield his power better. Anyone who can ascend to Russia's presidency (other than that ineffectual drunk, Yeltsin, who had the luxury of Western backing) and not only keep power for six-plus years, but strengthen his grip exponentially, has somethng of the archcriminal in him.
Trust me, Putin fears organized discontent at home far more than a "tarnished" image abroad. It's understandable why Russians would want some stability after a decade of Chicago-style gangland killings, and Putin understands better than anyone what people are willing to give up in order to get it. Eliminate street-level crime, and most Russians won't make a peep if you happen to clear out any street protests in the process. Especially if they know it might mean tossing back a vodka-and-cyanide cocktail one afternoon as a consequence.