Here’s the thing, the answer is entirely based on the world and magic system you’re hypothesizing, so there’s no fixed answer.
For example, in a Shadowrun world, assuming you could make it happen with a mass sacrifice or ritual magic, Turn to Stone is a channeled spell - the moment you stop concentrating, it ends, and they regain control. So no good there. Still pretty scare I grant.
While they don’t have a “turn to flies” spell, they did (different editions can be different) they did have “turn to GOO”, which was ALSO a channeled spell, but if the goo was scattered or dispersed beyond a certain range, well, so was the returned target. If “turn to flies” worked the same way, given the motility of flies, it would be the most gruesome and lethal option after a short period of dispersal. Paralysis would be the least effective, as it’ll again, stop the moment it’s channeled by way of comparison.
In 3rd Edition (or 3.5) Hold Person (for Paralysis) or the Mass Variant is a comparatively low level spell, so it’d be easier to fix (no one said your side was the only one with casters, so even a 2nd level spell can fix depending on type). Turn to Flies isn’t really a thing, so to get that effect you’re going to need the equivalent of a Mass Polymorph Other, Wish, or Miracle. That’s going to a very high level spell, and it’ll almost certainly take the equivalent to counter - unless it’s all illusion magic, at which point you’ve got some additional freedom in casting. Which is what I’d try to do.
Flesh to Stone for a Single Target is already a 6th level spell, so assume again a minimum of 9th level for a Mass Variant, at which point, you’re right back to using Wish.
And so on and so forth for any number of magical systems out there, and again, it presumes No One is shielding or counterspelling, or etc.
For that matter, if you’re a high enough level magician to cast these spells, it doesn’t matter if:
Heck, especially since they DON’T know you can only cast this once you are now the most wanted person in this world. Not only by the enemy as a WMD, but any other sovereign powers who want to make sure you NEVER can interfere. Whole city blocks if not whole cities are going to be obliterated just to get you.
Screw that, if I’m that powerful of a mage, I’m Getting the hell away because I want to live dammit. Teleport without Error, here I come!
If I must play nice with the silly hypothetical though, it depends on how long the spell needs to take effect. Given my control, I think turning to stone slowly, over say a period of 30 minutes, ideally from the feet up and letting all my enemies call and video call all their friends and loved ones while it works would be the most intimidating options.
Flies would probably look like bad CG, or too unreal and once the flies are gone, there’s no evidence left. And as for paralysis, it is good in terms of taking out more people to service, but less for absolute intimidation.