I actually never used to nickname my Pokemon but for some reason I decided to in X (which I got 2 days ago). Most are semi-random. Some I like though are:
Sham Wow - Chespin
Rule 34 - Ralts
First gen - Pidgey
Bouncin Boss - Azurill
Beeatch - Combee
Foamonkey, Fernmonkey, and Flamonkey - Panpour, etc.
P!mpslap - Riolu (they don't allow pimp I guess)
Math - Plusle
You PanDONE - Pancham
and my favorite: ur mum - Gulpin (you know, because Swalot hurhur)
Scatterbug= Scatman
Shelmet= Lancelot
Basculin= Randy (Randy Marsh from South Park)
Greninja= Frank (all frogs are called Frank)
Jynx= Helga
Poliwrath= Polly
Jigglypuff= Puffy
Lucario= Luke
Charizard= Rango (lizard)
Pawniard= Iracebeth (Through the looking glass)
Floette= Fleur
Tyrantrum= Dino
Delibird= Nicholas
And of course I trained Quacklin' to the top level
I'm posting a long-ish list of Pokemon I've named that I thought were pretty memorable throughout the Gens. Not all the Gen lists are long.
Starters:
Spoiler:
All are a variation of eachother, with the base name being from Generation III.
Squirtle: Neros, I learned later that it's the Greek word for water. Who knew?
Totodile: Neo
Mudkip: Nero
Froakie: Nelomar
Bulbasaur: Shiloh
Chikorita: Sora
Treeko: Shiro
Chespin: Shagohod (This one turned out to be my favorite Grass Starter).
Charmander: Wolfen for the first, Aznable for the Speed-based Son.
Cyndaquil: Wolfos
Torchic: Wolf for the first, Zero for the Son.
Braixen: Wovlar
Legendaries:
Spoiler:
Articuno:
1st. Celsius, Summon Spirit of Ice
2nd. Daimaru, Sumiyoshi from Excel Saga.
Zapdos:
1st. Volt, Summon Spirit of Lightning
2nd. Norikuri, Iwata from Excel Saga.
Moltres:
1st. Efreet, Summon Spirit of Fire
2nd. Toru, Watanabe from Excel Saga.
Mewtwo:
1st. Yuan, of Tales of Symphonia fame.
2nd. Twelve, of Street Fighter 3 fame.
3rd. Giygas. You cannot grasp the form of his attack.
Mew: Ness
Raikou: Raiden
Entei: Judgement
Suicune: Fujin
Lugia: Sylph, Summon Spirit of Wind
Ho-Oh: Aska, Summon Spirit of Light
Celebi: Mar, Time-traveling hero from Jak and Daxter.
Regirock: Tower
Regice: Justice
Registeel: Chariot
Latias: Martel, from Tales of Symphonia.
Latios: Mithos, from Tales of Symphonia.
Kyogre: Leviathan
Groudon: Fefnir
Rayquaza: Harpuia
Jirachi: Hylia
Deoxys: Tyrant
GEN I
Spoiler:
Caterpie: Degobah for Gen III. Darjeeling for Y. Wouldn't let me name it Degobah.
Weedle: Hedsonny
Pidgey: Roc, after the Persian deity.
Ekans: Lamia
Pikachu: Rogan
FemNidoran: Iori
MascNidoran: Krill
Clefairy: Cupil, from Skies of Arcadia.
Zubat: Ginovaef
Vileplume: Calypso
Meowth: Reno, after a cat my family took care of.
Psyduck: Ferriman
Growlithe: Ephraim
Abra: Kenshi
Machop: Shokan
Bellsprout: Wakaba
Ponyta: Sigmund, after the flaming lance from Fire Emblem: Sacred Stones.
Slowpoke: Osaka
Farfetch'd: Jayson, after Jayson Blair; discredited journalist from the New York Times. Wiki him!
Grimer: Plague
Gastly: Wight for the first, Burnie for the second.
Drowzee: Django, from One Piece. I watched the 4kids dub, so sue me.
Krabby: Zoidberg
Voltorb: Ululation onomatopoeia. Renamed Raymond for the sake of not being racist.
Exeggcute: Xel'lotath, from Eternal Darkness.
Cubone: Galimade
Hitmonlee: Bruce
Hitmonchan: Mac, from Punchout.
Magmar: Volvagia
Scyther: Dexter, from Dexter.
Tauros: Goht, from Majora's Mask.
Ditto: Your Cousin, which was humorous since it was my breeding whore.
Vaporeon: Undine
Jolteon: Okkusenman
Flareon: Lambda
Aerodactyl: Ridley, from Metroid.
Dratini: Romani
GEN II
Spoiler:
Sentret: Tomokazu, from Yumeria.
Hoothoot: Clear, from Final Destination.
Togepi: Genis, from Tales of Symphonia.
Mareep: Benimaru, from King of Fighters.
Bellossom: Lilo.
Yanma: Black Bomb. Long story involving a slushie with every flavor inside it and dragonflies being attracted to it.
Espeon: Jean
Umbreon: Dusk
Wobbuffet: Bianchi, when it was a Wynaut and cute.
Girafarig: Peanut.
Dunsparce: I'M SO SORRY (Wonder Trade).
Heracross: Honda
Sneasel: My real name, since it's my favorite Pokemon.
Skarmory: ShadowHawk, after the comic book vigilante.
Houndour: Colmillos, Spanish for Fangs.
GEN III
Spoiler:
Poochyenna: Barry, from Resident Evil.
Zigzagoon: Elliot for the first, Janine for the second. Both are from the game Blue Stinger.
Taillow: Maverick
Wingull: Colette, from Tales of Symphonia.
Skitty: Pollyanna, the song from the Mother franchise.
Aron: Burton, from Resident Evil again.
Plusle: Jade.
Minun: Toru. Both from Jackie Chan Adventures.
Anorith: Law, from Tekken.
Absol: Soma, from Castlevania.
Bagon: Icarus
Beldum: Sentinel
GEN IV
Spoiler:
Bidoof: Trash
Budew: Snow Pea, from Mucha Lucha.
Burmy: Deku
Lucario: Qui-Gon Jinn, from Star Wars.
GEN V
Spoiler:
Pansage: Ferb
Pansear: Phineas
Panpour: Baljeet, all three are from Phineas and Ferb.
Sandile: Crocomire, from Metroid.
Dwebble: Crawmad, from Pikmin.
Scraggy: O-Dog, from Menace II Society.
Sigilyph: Sumer
Emolga: Nonon.
GEN VI
Spoiler:
Fletchling: Ilpalazzo, from Excel Saga.
Pancham: Jet, from Avatar.
Furfrou: Mabari, from Dragon Age.
Espurr: Tersias, from the Shadowmancer book series.
Honedge: Cress, from Tales of Phantasia.
Hawlucha: Buena Girl, from Mucha Lucha.
Shit, that was a ride. Hope you liked some of the names.
[color=#9400d3][b] I find myself always naming my pokemon the japanese word of what they look or fight like. So i have Gardevoir name Utsukushii the japanese word for beautiful.