Hi, Jason, the Papers software has both desktop (Mac) and iPad version. They can sync without a web-based cloud reference library.
http://www.mekentosj.com/papers/
Currently, I’m using Papers to manage all my reference on iPad : export all my Endnote reference with their attachments, import into desktop Papers for Mac, sync Papers for iPad and desktop.
If Endnote can do the same, I’ll definite go for it without all the export and import …