The only thing I really need is having all the custom clipboards available under the Menulet; as drop-out lists and an organizer to move/edit and rename clippings. A lot of folks just don't use or like dashboard-like panels.

My suggestions are allowing for customization of what is shown under the Menulet. To make that Menuletlist shorter and have more space for the custom clipboards.
Everything except "Quit" should be under the "Preferences" tab. The "Application" and "Spaces" list should be optional. I don't see a use for them and they take up space under the Menulet.

Great would be if individual clipboards could be password locked, for storing sensitive info.

Overall I think the application is nice as it needs no application windows or floating panels if desired. I hate opening an application to access clippings, like many of the other apps require.
I still miss iSnip, but Clips could easily replace it if it allowed for a little more customization.

Thanks for your work!