Utilities never seem important until you really need them.
There is no "standard set" of utilities, just as there is no standard organization. Your organization, and the services it provides, define the domain of problems that are likely to need addressing. Build your utility chest with applications that meet your needs: accounting, advertising, artwork, . . . every domain has software that can provide a productivity boost to your internal processes.
For web development projects some of the layers that will need special tools include: