I never really bothered with nicknaming pokemon for the longest time, then I started doing Nuzlockes and actually got really into it I have a lot of pokemon now that I will always give certain nicknames too. Sometimes the nicknames are random, but other times I put lots of thought into the names. He are some of my usual ones:
Bulbasaur: Cabbage. Back in the days of Red and Blue there was a kid at school who told me he nicknamed his Bulbasaur Cabbage. When I finally got around to nicknaming pokemon, there was no other nickname I felt I could give it.
Wooper: Female = Natalie. No idea why. I just called one that once and it stuck.
Male = Newton. "Ned's Newt" is a cartoon about a kid who owns a gigantic talking newt called Newton who is blue. Hence the name. Sometimes I go further and change it to Isaac (as in the scientist Isaac Newton)
Fennekin: I love the Harry Potter franchise. One of my favourite aspects is the Patronus charm (if you don't know what that is, its a spell that forms into a silvery animal to ward off Dementors, hideous, soul sucking demons) - the Patronus forms into a different animal for different people and for the character Seamus Finnigan, it takes the form of a fox. So any male Fennekin I train is nicknamed Finnigan the Fennekin.
Swanna: Cho - similar to the above reasons, only this time because Cho Chang's patronus is a swan.
Misdreavus: Hermione. I feel like a lot of people do this, but I don't mind using someone else's good idea. Given that Mismagius is based on a witch and Misdreavus has a kind of mass of untidy hair, the nickname Hermione just seemed appropriate.
Mismagius: McGonagall: So sometimes after evolving, I switch the name from Hermione to McGonagall, simply because, as it is fully evolved, Mismagius is an adult witch, while Misdreavus is in school.
Piplup: Forster. This one takes a little more explaining. Empoleon based on an Emperor Penguin. The latin name for Emperor Penguin is Aptenodytes forsteri. The forsteri bit comes from Johann Reinholf Forster, a naturalist who accompanied Captain James Cook on his second voyage. In his time he made significant contributions to the field of Ornithology (study of birds) and named five other species of Penguin (Little, Chinstrap, Gentoo, Magellanic and Rockhopper) so what more reason is there to name Piplup after the guy?
Psyduck: Male = Ferdinand. If you have ever watched the film "Babe" about a pig who wants to be a sheep dog, you'll know about the trouble-causing duck called Ferdinand.
Female = Jemima. From The Tale of Jemima Puddle Duck by Beatrix Potter
Pidgey: Percival and Penelope... because they begin with P. No other reason.
Rattata: Joey. I really shouldn't need to explain this.
Goomy: Pancake. So I did a Wonderlocke on Y version wherein one of the pokemon I got was a Goomy named Pancake. Happily, it evolved into Goodra and survived right until the end. All other Goomys get named Pancake in its honour.
Espeon: Lucky. In that same Wonderlocke, I got a shiny Espeon who made it to the end, but came so close to dying so many times that in the end I began calling it Lucky.
Snivy: Mapleleaf. Again in that same Wonderlocke, one of the survivors was a Serperior that came with this nickname.
Deino: Blue. I also did a Wonderlocke on Alpha Sapphire and got a Deino named Blue. Blue did not last long, maybe half an hour before being murdered by a Sandslash. But the name stuck with me.
Torchic: Sanders. Because of KFC.
Charmander: Charles. Because whenever he's on the team, he's in charge. (Wonder how many people will get that!)
Tepig: Bacon. Because why wouldn't I?
Togepi: Twerp. Because I felt like it!
Koffing: Biohazard. Because it is.
Turtwig: Terrence. Because what other name is there to give a turtle without resorting to Ninjas?
Zubat: Sanguini. He's a vampire seen briefly in Harry Potter and the Half Blood Prince, and to be honest, Dracula and Vlad are too obvious for me.
Vivillon: Viola. You know why.
Pikachu: Ash. For the same reason.
Talonflame, Moltres, Ho-Oh: because they are all fire birds, like Dumbledore's phoenix.
Taillow: Rustic. Because the latin name for the Barn Swallow is Hirundo rustica
Ponyta: Lightfoot, who was the parent of Snowmane, King Theoden's horse in Lord of the Rings.
Anyway. Those are my main ones. Other pokemon I just name what I feel like naming them at the time.