I am designing a report building tool within a larger application because the users require the ability to create a large variety of customized reports.
To enable this I have decided to use an inspector that is used to alter any of the potentially large number of options, including display options and types of data. The inspector is sectioned off such that relevant types of options are grouped together.
The inspector as a whole is scrollable, some of the options within the inspector can have many items (possibly hundreds or thousands) that night need to be checked. This requires a scrollbar, but the scrollbar inside a scrollbar can cause havoc with the users (see: http://baymard.com/blog/inline-scroll-areas).