Somebody probably already lambasted Radical Dreamer but I have to throw my two cents in:
Metroid/Zero Mission:
Two Ridleys: Given that you can't stretch Ridley's skin over Mecha-Ridley I can only guess the latter was built for outer space operations and use the "Ridley" image to strike fear into Federation crews.
Metroid Prime:
The Orpheon is the frigate whose distress signal that Samus responds to. It is most certainly a Pirate ship (in-game scans and events support this claim) and they were rebuilding Ridley or attaching the leftovers to a cybernetic frame.
No Ridley in Metroid Prime 2, or Metroid 2.
I haven't played the third Prime past the introductory areas, but I can guess that if there's a phazon-infused Ridley that corruption would end when Samus destroys Phaaze (which I'm assuming she does; she has a habit of blowing things up).
Super Metroid: Either a clone or the restored original. Phazon survivors are granted an accelerated healing rate among other things. Mutated pirates dying when they stand on it notwithstanding.
Metroid Fusion: since it's possible that Ridley's leaving his DNA all over the galaxy (especially considering he keeps getting killed by Samus) it's entirely possible that the B.S.L. has a clone of him in cold storage for study.
As for who originally thought of using Metroids for power and weapons? The pirates.
Okay, so, it looks like I'm going to have money for MAGfest after all. I can probably swing taking the metro down to Alexandria, but that leaves the problem of rooming. Anybody who can put up with me, I'd appreciate it.
I know this isn't the best game in the series but it still needs a little love. I'm posting the source material for what I'd like to be remixed, though it's not as if I'm telling you guys what to do.
http://blue-bomber.jvmwriter.org/media/music/BattleNetwork/src_exe_bcc/MMBCC%20-%2011%20-%20Navi%20Clash!.mp3
Bye!
I'm still reeling from some of the challenges. I was only able to complete Target Smash level 1 in under fifteen seconds by watching a video on youtube and even then I still took three extra seconds over the vid because of poor execution.
Finishing anything--ANYTHING--on the Intense setting is going to be nothing short of a miracle, especially the boss battles..
On the other hand I seem to have figured out that you can trick the Alloy Fighters into suiciding in Cruel Brawl, but that damn Blue alloy fighter keeps using the Heel Kick before I can goad the essential fourth and fifth fighters into falling.
Patience and Perseverance. And Jigglypuff.