* ej.ru (assortment of articles by opposition writers)
* kasparov.ru (chess grandmaster and one of the opposition leaders)
* navalny.livejournal.com (possibly most prominent opposition leader as of late; mayor of Moscow candidate in 2013 mayoral election)
* grani.ru (opposition newspaper)
I'd have to agree with said elsewhere in the comments that an average Russian will likely not notice those sites virtual demise. They're not much known or popular outside of a tight opposition camp.
Echo of Moscow is, however, a very popular radio station. Banning their site is likely to cause a little shit storm. It is not banned though and working just fine. What happened is they hosted their own Navalny's blog [2] and this particular URL was banned. However, the banning system is IP based, so along with it all the site would have been blocked. The site admins quickly took down the blog and the ban was lifted.