This is a cool thread to resurrect.
It's so hard to pick just one: as a child I would have said Cookie Monster and Ernie. Now I would add Grover, and it's hard not to mention Big Bird, too (Kermit, too, of course, but he's not SS-specific). Having become a serious Muppet and Jim Henson fan the last several years and learning more about the dynamic between Jim and Frank, it's becoming harder for me to separate Bert and Ernie as a unit-- I now see them as a classic duo and can't really name one over the other as a favorite.