Do Evernote and thebrain/personalbrain have an "offline" mode? That is, can I keep things nicely organised locally instead of having to upload to the cloud? Evernote seems to suggest this is the case but at a very cursory perusal both seem to stop short of actually saying "you can use this to organise the files on your hard drive".
You can have local only, as well as synchronized Evernote notebooks.
The notes are search-able and files are embedded in the notes as attachments of a sort. It is not a file system organizer - it is more of a document database.