I don't have the equipment to fish for flatheads yet, so i mostly fish for channels. My favorite baits are hotdogs, bee-jay doughbait, and wheaties. On my setlines i like to use live bluegill or cut shad
my favorite bait at this time is cured liver i am going to try to start catching bream and bluegill to take with me when i go to nickajack or chester frost park hopefully that will work better than usual.
I'd have to say shad if I'm using cut bait, and bluegill if I'm using em live. Also, after a good rain I use nightcrawlers almost exclusively. I hardly ever use stinkbait or livers, cause I figure they are more likely to bite on whats naturaly in thier environment.
Bee Jay is a cheese based dough bait. (well at least thats what it smells like) It originated in Kansas and works good in local lakes and ponds. They don't have a website, but I am pretty sure that you can buy it out of the state of kansas.
I no longer pay for bait, so I'll have to agree with the cut skipjack. Today I hit the river around noon, and ended up with a 4lb channel, an 8lb flathead, and an 18lb blue - all on cut skipjack. Not only that, but it was frozen/thawed skipjack caught at the dam earlier this week. Second place goes to live shad (when they're running in the same place I'm fishing), and third place is a tie between cut shad and catalpa worms. I use bream when fishing smaller rivers for flatties.