I alternate each hook between live perch, and cut shad. If one seems more productive when I run the line, I may switch to one or the other. Just use what's available, and what they eat, and you will do fine. For me, and where I fish, I can find no valid reason to use something different. Bullheads can be good bait too. I just haven't had any luck on them like with perch and shad.
To me it depends whether you're targeting flatheads and large channels or not, live bluegill's the best bait for them; but's there's natural baits that are prevalent this time of year in every section of the U.S. i.e. grasshoppers, catalpa worms, and other insects that will catch all types of fish (using smaller hooks also). Sometimes I like to run a trotline with the idea that I never know what I may catch next (someone said, "the river's like a box of chocolates, you never know what you're gonna get".)
That depends on what your fishing for.
If your after smaller fish, And can get Grass hoppers this time of year. They are the best for say 10 lb down.
If you can not get them. Take shad and cut into the size baits you would like to use. Take a gallon jug Plastic or glass. Dig a hole in the ground, And place the jug with your bait in it and filled the rest of the way up with water. Put in the ground. And cover with something that will not allow anything to get to the bait. And also that will keep the cool air around the jug. In 24 hours your bait is soured but not rotten. It will or should have turned red, And have a smell to it. If your one that does not like to get the smell on your hands. Wear gloves.( doing the bait in the ground allows the bait to stay firm not turn into mush like it does out of the ground)
The fish are feeding on dead stuff and if some your catching have the Runs. You can bet they will tear this soured bait up.
This works with shad or skipjack. And buffalo or carp will also work.
If you have what there feeding on, You catch a boat load. But of your bait is not what there after, You will not do as well.
When we were fishing for a living we switched baits as soon as our catch started dropping off. We would start using different baits. and most times would bait every other hook with one bait, And then the next with something else.
The soured shad or skipjack will when cut into big pieces wear the big blues out also.
I use post hole diggers to dig a hole that just fits the jig. And I keep a 12"x12" landscaping block over my hole. We have a hole at the place down by the river, That is 25 years old.
There will be several things to consider when picking a 'best' bait. Here in central Arkansas, you can pretty well figure that cut shad or skipjack is going to get the most bites. From everything! I used to trotline the outlet cove at the nuclear plant near Dardanelle/Russellville/London continuously from early spring till the water got down low enough on the main river to jugfish...usually early June. The turtles in that cove were so happy to see me drive up that they'd all lay on the surface on their backs, clapping their flippers together, saying, "Yaaay, it's suppertime!" I'd bait up my lines with cut shad, and they'd have it stripped within an hour. Despite what's been posted here about catching catfish on a bare hook, I've always had the opinion, "No bait, no bites!" I had several lines out, and as soon as I finished baiting the last one, I went back to the first one and started rebaiting. Then I did the same thing a third time. By that time, the turtles were pretty well full, and they'd leave my bait alone so I could catch some fish. If I'd known about using chitlings for bait back then, that's what I'd have been using, because the turtles can't get them off the hook. No, chitlings won't get as many bites as fresh cut shad, but they will catch a lot more fish than a bare hook. The same thing applies to using soap for bait. It's a really slow bite; but, nothing but catfish will hit it. I've heard the same thing about mineature marshmallows, but I've never tried them, so I can't comment firsthand on that. So, if you have a problem with bait being eaten by something other than catfish, if you're only checking your lines once a day, the 'best' bait may not be the one that the catfish like the most.