Shelly: You know, she's in a shell... and it's a girl's name...
Zamboni: Double meaning time! First, a Zamboni is a machine who sweeps the ice of an ice rink. My Zamboni is a sweeper who can handle Ice with Focus Blast. Second, Alakazamboni.
Dreistein: Sp. Atk is actually mental power. Since Einstein had huge mental abilities, I called her Dreistein because she has three heads. Oh, and its moveset is based of Ghetsis's Hydreigon.
Ononx: This is just a reference to Ononokus, which, when you say it quickly, sounds like Ononx. I like its Japanese name more than Haxorus.
Grimesley: Got it?
Bizarr: Just look at it.
Yamaha: That's fast too.
Beep: Magnemite's cry sounds like beeping. That's why.
Rocky: You see that thing on top of it? It's called a rock.
Judith: Judo + female. Figures.
Sparta: I wanted to name him Madness first, but hey. Now I've got a reason to use
Aquasha: Aqua + quash + a (the 'a' because female names often end with an 'a')
Maiden: Inspired by a certain episode of the anime.
Windie: That's just its Japanese name. It fits a female Arcanine.
Samarium: Obviously named after the element samarium; chosen because it sounds good for a Gallade. Maybe because it sounds like 'samurai' to me.
JellyTime: It's peanut butter jelly time! Because this Shiny had Quiet nature and Cursed Body, I decided to train it to a Jellicent, and I didn't wanna stop till it was lvl. 100.
Quercus: That's Latin for oak. I worked together with two friends of mine: we each trained one Simi. If only Multi-Triple Battles were possible...
Billy: Immediately when Elekid hatched, I thought of Billy. Don't know why, but maybe Billy the (Ele)Kid?
Articrash: Artic + Icicle Crash.
Rain-team nicknames & explanations
Crazy Frog: That lunatic frog who has nothing else to say but ring-ding-ding. How awesome is that guy!? The one Pokémon a rain-team can't live without nowadays: Politoed. And it does what it's made for: Drizzling. And owning with a Specsitoed-set.
Galatea: Found this one on the web. Sound a-w-e-s-o-m-e. Empoleon is quite good. I'm suprised that I've overlooked it for so long.
Cirtcenam: Manectric backwards. Hurray for originality! Same story as with Empoleon: overlooked, but epic. 'Cuz you know, no single rain-team should be without an Electric-type. Thunder FTW.
Nachos: I'll say: bring in the tacos, burritos and salsa dip and let's have a Mexican party! Best rain-wall in existence.
Kabutops: Sorry, no nickname. I found a Adamant Kabutops on Platinum and transferred it without nicknaming. Ah, well. Kabutops is a nice Physical Water.
Toxicroak: Trained this guy on Platinum too, 'cuz I wanted Drain Punch without having to breed. Yeah, I'm lazy and I know it. Toxicroak is quite awesome in rain thanks to Dry Skin. Combine that with Life Orb, and you'll have boosted moves without HP depletion! W00t!