I always use deminutive of my real name. (Which I use only in ironic connotations and feel awkward IRL when someone calls me that - meaning it not ironically).
And then I walk the Pokéworld and everybody calls me with deminutive.
I mostly use my real name, but I may add an extra ''H'' in order for it to sound like english.
Except when I'm playing as a girl, when I do that I usually research into name meanings and shit.
I took a look at my games in order of when I got them and it turns out I alternate between using the Pokemon Special character names, like Red and Gold, and using the shortened version of my own name, which is Tony.
I actually put a little thought into the name for White 2. In White my character was known as Tony so I thought for a while wanting a name that alludes to Tony but is also new and different. I came up with Newton which I felt rather happy with.
I use my internet alias: Dragey which itself is based off the word Dragon.
I always use my real name.
I use my real name now I used to use 3X as in Triple X because I though it was cool but I was 10 at the time :P
I generally just stick with the character's official name... Unless they don't have one. In that case, I'll call them Ookalf. [/boringanswer]
I haven't used my real name on Pokemon games since I was 12. xD They tend to be names of characters I've created or just names I like.
For example, here are my list of current names I'm using in each game.
LeafGreen - Karla
Platinum - Lycoris
SoulSilver - Lyra
Black (storage version) - Misaya
Black (regular playing version) - Alyssa
White - Olivia
White 2 - Ruslana
Funnily enough, Lyra is the name of a character I've created for a story, and I didn't remember that it was the default name for the HGSS female protagonist until after I gave her the name. xDD
Real name. If I ever hypothetically played as a female, Id use the feminie counterpart to my name, Kathy.
I prefer to use my own name. I like to imagine myself as the PC, so naming them after myself adds to that. The few times that I've chosen the female PC, I would either choose the female version of my name or the girl's official name.
I tend to make up names that fit their looks/personality. I can't use my real name because I'm not a girl.
FireRed: Emily - She just looks like that to me. Seems like a name for a girl who is both pretty and tough.
HeartGold: Serena - Seems like the name of a quiet girl who is very innocent.
Emerald: Brianna - Tough girl who is not afraid to get rough.
Platinum: Melody - Very girly girl who goes for the cutest Pokemon she can find. (Which is why most of my Platinum team at least started out cute.)
White: Alexis - The name always sounded kinda sexy.
White2: Lacey - Another quiet, sweet girl.