Absolutelybloody essential:
ToolsDaemon
NewIcons
KingCON
CyberGFX
SFS
If you don't know these, you must be some kind of Windows user.
Other very useful utilities:
XAD - a general, open-ended dearchiver. Included in OS 3.9 and MOS.
Starclick/Noclick/whatever - stops that annoying floppy clicking.
IDEFix - enables ATAPI support on Commodore's braindead IDE controllers.
ASLPatch - this has been amended in newer OS releases, but I still run OS 3.0. Haven't had time to install this OS 3.9 CD... ;-) Basically allows you to set up the default size and position for ASL file requesters.
Oh, and I've got a similar patch to make all requester appear below the mouse pointer, whose name I've forgotten.
I've also got some bauta replacement for the commands Copy, Delete, Makedir, and a slew of other C= file manipulation commands. Can't recall the name right now, but it adds such essential features as a Move command and automatic dir creation.
ARen is a very useful filename manipulation program.
Really, I use the Shell a whole lot (made so much nicer through KingCON), but using a rather conservative choice of commands, but enhanced through a lot of aliases and some scripts. I really wish I sat down one day and learnt ARexx, too. There seems to be so much potential there.
Still, the original set of Commodore tools are very competent, but sometimes they need a patch here or a replacement there, or perhaps a new datatype or filesystem, but basically, they provide a working paradigm which I really like. Therefore, most of my WB enhancements are just patches, aliases or extensions, and not any new-fangled parts. The contents of C: and S: do it for me.