Yeti and Stop Smiling are good magazines -- I like the books Yeti publishes too. n+1 is also pretty good.
Harper's is the only magazine I read cover-to-cover (except for the Lewis Lapham piece, which seems to have been the same article since 1997, with some minor changes).
I usually flip through The New Yorker, The NYT (both my wife's subscriptions), BOMB, American Theater, and The New York Observer (free subscription). On rare occasions I've been known to flip through The Atlantic, The Nation, New York, Viorety, EW, The Comics Journal, and Wizard.