OS 3.1 has some bugfixes like support for graphics card drivers Picasso 96 and Cybergrapx. Kickstart 3.1 lets the HD waits a little longer to boot up, this is need it for slow spinup HD's.
You also get more datatypes and a free cdfilesystem too. The CDfilesystem has some flaws, not every Amiga CD-ROM could be read.
You can also run wb 31. on kickstart 3.0.