Viacom has issued a pretty solid response (PDF)--that they issued no such DMCA notice, and if they had, YouTube should have notified the user who submitted the clip and given them a chance to file a counter-notice. Viacom further stated that they found the clip elsewhere, reviewed it, and agree that it constitutes fair use of their content and should be put back up. (YouTube has put the clip back up.)
This is not good news for YouTube--this is further evidence that they are taking down content without receiving DMCA notices, which means that they are exercising editorial control over their content, which places them at greater risk of failing to successfully defend their claim to be protected by the DMCA's "safe harbor" protections.
Other such evidence comes from Mark Cuban, who has been issuing DMCA subpoenas to YouTube users who have used his content (movies produced by his companies such as HDNet). He has also issued takedown notices for some such content, while explicitly choosing not to issue takedown notices for others--because he wants the promotion from YouTube, just not wholesale theft of his content. Yet YouTube has taken down clips that he has specifically chosen not to issue takedown notices for.
This looks like a misstep for the EFF.
UPDATE (March 28, 2007): As noted by commenter Jamie, there apparently was a DMCA notice issued by BayTSP, which was hired by Viacom to send out DMCA notices on its behalf, so Viacom may not be in the clear.