3.9 is great if only for the fact it supports JPG workbench backgrounds out of the box.
..of course there's other nice stuff, built in archive handling app, AmiDock, GenesisTCP stack, MP3 player, click and go CD drive configuration... If you don't want to spend hours getting a barebones 3.1 system usable, 3.9 is the way to go. I only go with 3.1 when I'm stuck with low memory.