I used to bunch together by series and faction, arranged all pretty like in neat lines etc. Classics Autos and Cons were facing off against each other weapons drawn and so on.
But now I subscribe to the Botch-the-Crab school of TF arrangement, which can be best discribed as "all mixed up." A G1 figure beside a ROTF figure, beside a TFA, beside a BW. Decpticon beside Maximal. Robot beside an alt-mode, beside a beast mode. Some with weapons, some without.
Much the same as Botch, I find that I now pick them up more and transform them more, rather than being more worried about things like cool poses, facing-off-against-each-other arrangements, or segregation by series that influenced my TF collection before.
Only exception is G1 Dinobots who still have a shelf to themselves. 
PS- really should post some pics one day...
TF Figs of 2024:
1) Legacy Magmatron
2) Legacy Gears
3) SS102 RotB Optimus