I went with 'other'. I'm only just starting out with the whole 'display' thing after buying my first cabinet recently. Before they (the ones I've opened and played a bit with) were just out on a desk around the computer and then when we moved back they were on my clothes chest.
I've got 1 ikea detolf with metroplex standing on top, my 'big' MPs grimlock, YOTH prime and ultra magnus on the top shelf, the autobot car MPs on the next shelf with the trailer (and some supernatural phenomenon investigators at the moment) on the next, then my decepticons then autobot generations.
So it's kind of by size, line and faction all at once
it looks pretty full now, and i've got more waiting in boxes and tubs to go somewhere haha :/