Long post incoming.
More often than not, my names come from constellations or planets or something, if I'm really putting effort into the team. Most of them are pretty obvious if you just look it up; most recent names:
Zoroark: Vulpecula (Fox)
Gyarados: Volantis (Flying fish)
Manectric: Sirius (This one's not so obvious; Sirius is the pet dog of the hunter Orion [also a constellation] and the brightest star in the sky)
Formerly Pikachu: Carina (Also not obvious cause Pikachu was hard to find something for it; Carina is a keel which is basically the hull of a ship and what holds it all together. In this case, Pikachu was the reason I made the team)
Darmanitan: Aries (Ram, cuz super strong physical attacks; yes, it's a stretch, I know.)
Ferrothorn: Scutum (Shield)
Mienshao: Libra (Scale, representing balance, since the fighting type has a few heavily implied references to being as close to the "light" type as Game Freak was willing to get in 5th gen)
[u]Others I may have used[/u]
Scrafty: Lacerta (Lizard)
Galvantula: Aranea (Big spider, more or less)
Milotic: Aquarius (Water-bearer; alternatively, I sometimes used "Venus", which more or less went hand in hand with Milotic's inherent beauty aspect)
Weavile: Orion (Mythological hunter; further emphasized by my use of Pursuit << >> though, I may use this name on other pokes too, immediately, Bisharp comes to mind, along with Terrakion and Groudon)
Blaziken: Fornacis (Furnace)
Liepard: Leo Minor (Small cat, or lion, I guess)
Staraptor: Altair (Eagle, probably better used for something like Braviary but I just like the name in general anyway)
[u]The [s]six[/s] seven dragons of Deltora[/u]
(Yep, totally original, but this was too good to pass up as a naming theme for mono-Dragon)
Kingdra: Veritas (My most often used alt name, and for good reason. I like how it sounds >_> No but really, Veritas is the amethyst dragon, and shiny Kindgra just so happens to be purple.)
Salamence: Fortuna (Dragon of the lapis lazuli; that is to say, blue. I also just like the sound of this name.)
Dragonite: Fidelis (Dragon of the topaz, which is generally yellow or orange.)
Hydreigon: Honora (Dragon of the emerald; shiny Hydreigon is mostly green.)
Latias: Joyeu (Dragon of ruby, surprise, red! Also means "joy", obviously, and just look at its cute little face <3)
Altaria: Forta (Dragon of the diamond, generally white and extremely hard to break. Cotton Guard, anyone?)
Naturally, I can't fit 7 Pokemon on one team, and to even use the last dragon, it'd have to be in Ubers, cause short of Dialga I'm not sure who would represent Hopian, the Opal dragon. But there's another one I guess.
[url="http://en.wikipedia.org/wiki/List_of_Deltora_Quest_characters#Dragons"]http://en.wikipedia....racters#Dragons[/url]
For reference.
The seven names also have their own meanings but I couldn't really find a way to make them apply, short of Latias'. Hers was just perfect.
Veritas: Truth
Fortuna: Fortune
Fidelis: Faith
Honora: Honor
Joyeu: Joy
Forta: ...I don't remember this one. Will, help me.
Hopian: Hope
Needless to say I really love this series.
[u]Names I just use cuz wynaut[/u]
Kyurem: Void (It represents the absence of Yin and Yang, which says enough to justify the name, I think)
Alakazam: Mindfreak! (...speaks for itself)
Breloom: Bellum (Latin for war, last I checked, and it sounds similar to Breloom as is)
Porygon2: Analysis (Considering its background, that alone is enough, but also its abilities: Download and Trace [Not to mention [b][i]Analytic[/i][/b], hurr])
Serperior: Emerald (cuz green and based off the emerald boa, loosely)
Cresselia: Celestia (Favorite legendary gets an epic name, easily. Legendary based on the moon, so it fits)
Darkrai: Nightmare (If you have to ask, just move on)
Volcarona: Atlas (Same reason as Serperior, comes from what it's based on; the atlas moth)
Bronzong: Clear Bell (also obvious, based on the item with the same name in G/S/C)
Weavile: Mephiles (Weavile and I have quite a history, to be honest. I started with a typical "Shadow", then moved on to something at least somewhat more original in "Midnight", and then before the constellation thing was "Mephiles." See [url="http://www.sonic.wikia.com/wiki/Mephiles_the_Dark"]this.[/url] I think the connection can be drawn, if somewhat loosely.)
Mismagius: Missy (A pet name for my dearest favorite Pokemon)
Lapras: Railynn (...Honestly, I saw someone using this as a username a very very long time ago and liked it. Sounded like "rain" to me, so Lapras gets the nice-sounding name)
Pre-constellation Manectric: Ixion (Lightning-based summon in Final Fantasy X [among other FFs, maybe?] that took the form of a lightning horse)
Froslass: Shiva (See above, except, Ice-based and not a horse)
Uxie: Knowledge
Mesprit: Emotion
Azelf: Willpower (These three were back in 4th gen and if you don't understand I should hit you.)
Sceptile: Hayashi (Japanese for forest, I sometimes used Silva instead as the same end result, but Latin instead. THAT'S RIGHT WILL I DID THIS BEFORE I KNEW YOU EXISTED)
Empoleon: Neptune (God of the sea in some culture, I sadly can't recall atm)
Victini: Tsuna (Reborn! reference hardly anyone will understand)
Lilligant: Princess (obvious)
Sawsbuck: Sawsbuck-Win (Yes, that's right, I change it to Winter form and just leave the name. It's good enough)
Chandelure: Insidias (Trap, Shadow Tag. Enough said, though it still fit before when I used Flash Fire, because one would assume it has Shadow Tag, resulting in DOUBLE the trap!)
Raikou: Klystron/Kaminari (I switch between these two rather unstably, Kaminari being the obvious: Thunder; Klystron was something I heard ONCE, and only ONCE, and was like hey this sounds like Electron but better! [I also used it as the name of a Raikou evolution I spawned in an old fanfiction that.. Well, don't ask])
Suicune: Aurora/Borealis (Either one is painfully obvious and unoriginal. It's the reason I stopped using Suicune on one of my teams)
Metagross: Platinum (Shiny form. Enough said)
Noctowl: Nocturne (Also relatively obvious)
Virizion: [url="http://www.youtube.com/watch?v=DqUYNjFQ_qY"]MyBoots[/url]
Absol: Disaster (Even more obvious than some of the above)
Giratina/Giratina-O: Renegade (Same source as Absol)
Dragonite: Kairyu (This was before I spawned the seven dragons thing; Dragonite's japanese name sounds so much better)
Aerodactyl: Phobos (One of Mars' moons, means "Fear")
Celebi: Serenity (...I honestly don't know, it just seems fitting)
Swellow: Zephyr (Wind-based name for a flying type? No way!)
Jirachi: Wishmaker
[u]And the naming scheme I use for most others because if I kept going with the above section I'd never stop[/u]
Generally, if all else fails, I spawn a name based on the pokemon's type or design. This often results in really bad names. Examples:
Moltres: Blazewing
Rotom-H: Firebolt (More commonly I just use Plasmabolt for any of the Rotom forms)
Carracosta: Kabutops 2.0
Sigilyph: Xatu 2.0
...yeah, I should stop this now.
inb4edits.