Thing is, the memorable ones on the list aren't memorable just because they wanted to blow up the world, but because of what else they brought to the story.
Cell & Buu: Boring supervillains.
Johann: A lot was made of his desire to end everything, but the fact is that he never comes anywhere close to doing that (really, to doing much of anything on more than a small scale) during the story. What Monster's tension comes from is not the threat Johann poses, but the mystery: who is he, what made him that way, how does Nina fit in, and (most importantly) what is it going to cost Tenma to undo his "mistake?"
Rau: Was actually diminished when his agenda was revealed. Like Johann, he's a big mystery for the bulk of his series, but unlike Johann, he has a pretty minor presence during most of the story, disappearing completely- from the screen and from viewers' minRAB - for a lengthy stretch in the middle. Then during a single episode, it's revealed that he's just a psychopath who wants to kill everyone, but not for anything directly connected to the overall storyline, but because of a peripheral subplot that was introduced in that same episode. And from that point on, he's the main bad guy, more so than any of the other characters in the series, but his former suave, collected demeanor has been replaced with barely-coherent raving, random acts of violence, and a mask fetish. Not integrated into the story very well at all.
Frost Brothers: Mostly distinctive because they were Gundam prettyboys who were villains instead of heroes. They worked well enough for the series, but weren't what sticks out in my mind when I think of Gundam X.
Ginghnam: Argh. This guy's like Rau, except with even less presence in the story. Easily the weakest element of Turn-A.
Knives: Actually has very good reasons (along with all the other Plants who join him) for wanting to annihilate humanity. He himself isn't all that interesting - his role mostly consists of blathering about exterminating the vermin, your cause is hopeless, etc etc etc - but the changes humanity has to make on his account are the focus of some of Trigun's most memorable scenes.
Legato: Forces Vash to kill. Awesome.
Kotomine: Is less memorable because of his evil plan than because of how thoroughly he deceives everyone (not only is he actually a bad guy, but he's also a participant in the event that he's supposedly just refereeing - oh, and he has been for the past ten years, hurr hurr). He's much more of a standout in the F/SN game. In the final route his hand is tipped almost immediately when his Servants are killed, and yet Shirou has to seek help from him a couple of times, fully aware of what he is. A lot of time is spent inside of Kotomine's head, exploring his background and how he's had to deal with his unusual circumstances, making you see him very differently when he's just been a one-dimensional villain to that point. Hell, eventually Shirou (mister I-will-smite-you-for-great-justice) has to admit to himself that he actually likes the guy.
EDIT:
TL;DR version: Villains who want to destroy everything can be interesting, but wanting to destroy everything isn't what makes them so.