I don't usually name my pokemon except for in my Platinum. The only good names were Inferno for my Infernape and Gordo for my Snorlax. My Torterra's name is Twigy but that kinda lost its glory after Turtwig evolved...
Depends, Some pokemon I see a resemblance to other people or characters in games, books, or other media.
My Marowak "Flint" and my Heracross "Duster" are both named off of two of the main characters from the game Mother 3 for example. I like them both a lot so I decided to make a tribute to the two greatest characters of all time.
Sometimes I just go with something that sounds amusing, or I add on honorifics. For example, a Tentacruel named Tentchan.
For others, however, I go with references to other media or mythology. Like a Jigglypuff with Sunny Day and Solarbeam named Amaterasu, for a mythological reference, or a Slowking named Namor, for a comic book reference.
I either name them I thought was awesome from whatever I'm into at the time (I once played a fully Star Wars themed game) especially from animes, choose something meaningful to me, or just make something up on the spot that randomly fit that mon.