General

@GoldenHedgy: Lol. I don't name my Pokemon but I do call them nicknames sometimes.
Like I called my Ivysaur "Ivy."

I nickname all of my "first catch" pokemon in each playthrough :> Even the ones that sit in my box for a long time because I know I'll battle with them all sometime. I usually don't when I'm breeding, or when I specifically caught it to be traded away.

I used to never nickname them but now I got this new obsessive complusiveness problem that I even ask people to nickname the Pokemon for me before trading.

When I'm breading the same Pokemon (eg: 30 Charmanders) I nickname my Pokemon: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, AA, BB, CC, DD
There is 30 rooms in a box so I go up to DD.
It is an easy way to know what Pokemon is what breed, I usually write them down what IV one Pokemon has, what good nature it has and gender.
The ones who are bad I throw them away so I end up having like only 3 guys and have like: J, N, W left and repeat the cycle.

For my main party guys I do rename them if I know the Pokemon normal name.
Like everyone in 1st gen I nickname since I know what there names are.
Few Gen 2 and 3 Pokemon I nickname.
Gen 4 Pokemon I nickname 1 or 2 (like Rotom I will nickname since I know the real name).
I haven't nicked named a gen 5 or a gen 6 Pokemon yet.

Yeah same clean Pokemon is good.

Except when I had to catch 50 Pokemon in one day for Black & White 2, in which I just called them Penus, Ben Dover, Fat China, etc.

I like having clean Pokemon. Blaziken is Blaziken. But sometimes when I'm bored I'll give a different name to every single one of 'em.