Running Mountain Lion 10.8.3 I find that after a recent reboot my Favorites have all disappeared from the sidebar in Finder.
Finder > Preferences > Sidebar shows a number of boxes against Favorite folders, but these can not be selected
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Hold together Option+Command+esc and then relaunch "Finder" that will solve your problem instantly. If the problem persists, please try reinstall Mac OS X by Command+R after rebooting.
Try simply hovering over the heading "Favorites" in the sidebar and then on the word "Show" which appears to the right
This toggles the favorites on and off...
I had same problem on Yosemite. Hovering over "Favorites" and clicking "Show" worked.