My top five (minimum on every 3.1 rom'd machine):
1) Internet bundle: Yam, Ibrowse, tcp stack (Miami, TermiteTCP, etc.)
2) WB Enhancers: Magic User Interface plus either Magic Workbench or NewIcons...or GlowIcons if you install OS3.9
3) WHDLoad: absolutely brilliant harddisk launcher for old floppy based games...a must
4) Misc utilities: MagicMenu, KingCON, Arc, FBlit, Executive, BlazeWCP, etc.
5) CDROM driver: AsimCDFS, AmiCDFS, etc. and maybe a burner program if your cpu is up to it (BurnIt, MakeCD, etc.)
*Optional (hardware permitting): RTG software (CybergraphX, Picasso96) and WarpUp w/ or w/o Warp3D