National Dex order, but only in spots for the last Pokemon in each evolution chain. Afterwards I have the special guys, sgoing with all different Unowns, then in-game trades, Event Pokemon (if they aren't in the National Part like Darkrai is) and then my personal favourites, basically all of my trained, in-training, high levels and just those I've grown a special bond with (I get TOO attached to some of my Pokemon )