It depends on which fish I'm after and how I'm fishing.
For pike fishing with a float (or icefishing on a deadstick), since they usually hit the baitfish broad side, I hook them through the mouth with a stinger hook right below the dorsal fin (don't go too far below the dorsal fin or else you'll hit the spine, which would give you a paralyzed bait
)
If I jigging for walleye or bass, I use a smaller minnow and hook it through the mouth. This gives the most natural action.
If I'm deadsticking for walleye through the ice, I will hook the bait just under the dorsal fin. This allows the minnow to have the most natural action. Even if it is dead, it hangs a little more horizontal than a lip hooked bait.
I guess it all depend on the biting habit of the fish and the technique you're using.
I know some people here will tail hook a minnow when fishing under a float or deadsticking through the ice. The idea behind tail hook is to have the bait always digging for bottom. To do this, it is ideal to have the minnow is suspended a foot above bottom. However, this technique put a lot of stress on the bait and hence, your bait will not last long due to exhaustion.