Fish aren't the only animals that demonstrate this shaking. If I recollect, it's somewhat analogous to a release of autonomic nervous "energy" (not a mysterious energy, simply chemical reactions that generate the electrical energy by which the nervous system functions). I've seen it most pronounced in cattle. I have never seen it in any animal, including horses, that are euthanized with an overdose of anesthetic.
Not all fish are completely ectothermic.
You are right about big fish. Something like a bat is necessary, and some fish have THICK skulls!
My whole point, and my practice of what I preach, is to reduce suffering. As the person who carries out "the executions", I believe that it's my responsibility to essentially man up, buck up, shut up and do it HARD. When it's done right they'll never know what hit 'em.
Oh! One little caveat - if you're whacking fish that have an extensive bacterial infection, it tends to really soften their bodies. Be careful whacking those ones, as they tend to... splatter rather easily. :| (mmm, lovely!)