I didn't feel like putting my response in a comment, not that I'd have enough space, but here's how I order my moves:
First are the Status/boost/setup moves, you know, Thunder Wave, Trick Room, Swords Dance, that crap. Protect or Sub would also go there.
Then go attacks, arranged generally in order of PP. Close Combat and the like would tend to be last. With multiple 8 PP moves, the one with higher base power would go last. Because I easily forget the PP of any move that isn't 8 or one of the "staples" like boltbeam, that's why I say generally. If Earthquake goes before Crunch, ah well. Those 80-90 BP moves with 15 or 20 PP throw me off easily. In my mind, I kinda just lump them as "lots of uses" whereas Close Combat is.. yep. Few uses. Nothing sucks more than burning through your precious Stone Edges on those fucking Pressure legendaries. Damn you Zapdos! Damn you 80% accuracy!
Then, if I even have it, my recovery/suicide move. Perish Song also fits that bill. Sleep Talk will be placed before Rest as though it's an attack, so Surf and Ice Beam would still go before it.
For a guy like Gyarados or Breloom, it'd go Dragon Dance > Taunt > Attack > Attack and Spore > Substitute > Leech Seed > Attack, though in Breloom's case I haven't liked using the Subseed set in a little while, and in some cases I'd even forego Sub so I could have both Seed Bomb and Stone Edge.
None of that applies ingame.
A personal friend of mine is also into Pokemon and occasionally I would hack his teams for him; on one such occasion he was looking at the computer screen while I ordered his moves and he saw that I put them in a different order than he listed them to me, asked if I did it on purpose, and so without actually saying what I posted up there I basically said I had a way I liked to order my moves. He thought it was really strange, but interesting enough that he tried to figure out my motive and guessed how I'd put them. Not incredibly hard.
..ah yeah. Kinda a long-winded response, but that's actually one of my biggest quirks in Pokemon, or rather one of the only things I care about enough to implement in my hacks, given the chance. Nickname and shinyness don't matter to me and I almost never nickname my guys. Nor do I care where I caught my guys or when/where the egg hatched if I pokesav'd them. The only thing I put thought into apart from clicking a box here or typing a number there is move order.