I tend to nickname Pokémon an alteration of their actual name. For example, Ampharos would be Rapharam. Kinda like that. Or, if it just sounds kewl at the moment, I'd also use it. Like Zemquick, the Luxray (named before I found out it wasn't all that fast). I suppose I'll list my cooler nicknames that I've done:
Diamnaga, Dialga
Patiku, Pikachu
Bloo, Empoleon (I just like that one ^^)
Pialkia, Palkia
Tartynitar, Tyranitar
Skyblade X, Skarmory (only because I could fit the 'X')
And so on.