According to Mensa, the group for those who can score in the top 2% of a standardized intelligence test, the highest profile Mensa member (the group emphasized 'fictional' member) in the cartoon Simpson family did not top the members' list of favorite characters on the long-running Fox show. Perhaps not so surprisingly, that honor went to Bart, who one respondent dubbed "a hero in a way--in trouble and funny, yet good at heart and lovable."
Mensa polls its members monthly for a top 10 list on various topics and publishes in in the membership newsletter, the Mensa Bulletin. For those few nonmembers among B&C's readers—present author included—who won't be getting the Bulletin, here are the other nine.
Homer came in at number two in the poll, with Lisa grabbing the third spot. Rounding out the top 10 were Marge Simpson, Charles Montgomery Burns (Mensa gave full names, of course), Apu Nahasapeemapetilon, Maggie Simpson, Nedward "Ned" Flanders, Herschel Schmokel Pinkus Krustofsky aka Krusty the Clown, and Barney Gumble.
According to the Simpsons wiki on wikia.com, Ned Flanders is also a Mensa member, per the Idiot's Revolution episode, as are Dr. Hibbert, Professor Frink, Comic Book Guy, Principal Skinner, and Lindsey Naegle.