I'll second what Cory said: Excellent! And seems like another (must be a million of them!) super review of Onyx. Make me real happy, considering how many times on this site I have recommended Onyx.
Regarding what one can run in Onyx, I always run Repair Permissions on each of my Macs once a week, as part of my weekly disk cleanup/maintenance/repairs, and backups. In fact, I just completed it for both of my machines. I run Repair Permissions twice, as its seems on the first "pass' not all permissions get repaired. Also, supposedly ever since El Capitan came out, repairing permissions was taken care of by the Mac OS. Well, that is certainly not the case, at least what I saw for El Capitan, and continue to see in Sierra.
The other things I run in Onyx are:
1. Under Maintenance:
A. Maintenance on Scripts (Daily, Weekly, Monthly scripts)
B. Rebuilding some functionality (LaunchServices, dyld's shared cache, XPC cache, CoreDuet database, Mac Help, and Localization of folders' names)
2. Under Cleaning:
A. Trash.
B. Misc. (Delete: Automatically saved versions of the documents, Saved application states, Recent Items, Recent Conversions in Calculator, Items in the Mail Downloads folder, Items in the Saved Searches folder, Obsolete Items, My Computers list in Screen Sharing, Quicktime Content Guide, Contents of the Xcode Derived Data folder)
C. Logs. (Delete: Log files, System archived logs, Instant message logs, User Diagnostic Reports, System Diagnostic Reports, Mobile Devices CrashReporter)
D. Fonts. (Delete the fonts cache: System, Users, and Apple applications, Adobe Systems Incorporated, Microsoft Corporation)
E. Internet. (Delete: DNS Cache, Browser Cache, Download cache, Documented items list, Browser History, Recent Searches, Webpage previews)
F. User. (Delete the cache: Applications, System Preference panes, Audio Units, Java and Java Applets, Desktop background, International preferences, Dock cache, ColorSync, QuickLook, Temporary Items, IconServices)
G. System. (Delete the cache: Boot, International Preferences, Quicktime components, Audio components, Other system components)
For some of those, there are other choices listed. Also, I wonder if the Browser cleaning is just for Safari, which I rarely use. And, similarly for Mail downloads (I use Outlook).
I have been doing that for so, so long, never had an issue, and is like second nature to me.