In general, I wish there could be more robust search, including search of meta-data on notes (e.g., searching for notes that came from a certain web site).
More specifically, I wish there was a way to determine if a note has been internally linked to another note.
Finally, it would be very very handy to have some sort of notification that a note you clipped has already been clipped before. The "Related notes" feature sometimes helps with this but is not that reliable.
I love Evernote, but I frequently hanker for these features. Thanks!