Obviously it doesn't matter on a round plastic worm, but when using a lizard, sweet beaver, or similar plastic bait, is there a rule of thumb that says whether the point of the hook go on the top or bottom?

Hook on bottom or underside, most baits will turn hook down if you place it top or bottom any way.

yup

they do

This is true

If I rig a big EWG hook on the bottom of a lizard (so the point is on top), the lizard will flop over on its side.

You can try rigging it in the side, I read some where that it give's your lizards a more life like swim.
Duane

Bottom.

Bottom for sure!!!!

It'll do the same thing if you hook it on the top.

If they have a flat side to them, I will hook on that side. I like to hook them on the side away from the ripple tail if they are round.