I voted by line, but really by faction, and then basically whatever I feel like. Lines like Animated and AEC, where I don't really have enough toys to make a full shelf, tend to get put with the CHUG figures, making the longest and most ridiculous acronym ever. Similarly, all movie figures get grouped together.

If anything, I differentiate more by scale than by line. I know that sounds nuts for a TF collector given how loose TF scale is, but I tend to assume robot mode scale, at least, is consistent (apart from outliers such as Metroplex) and represents the actual relative size of the bot. Thus, Masterpiece and Alternators group together pretty well, as do most mainlines and CHUG. Then you have Cyberverse/pre-2012 Legends class figures who are the smallest. Modern Legends get put with their line because they are more like basics than Legends class toys.