Right now I am using OneNote only at work, as a corporate wiki. That works quite well, because a its syncing/conflict/linking capabilities seem to be more related to the task.
I had the problem you describe with Evernote — I had a lot of notes, and I wanted to create some structure for them, beside just search. Something like “Index” pages for subjects. To tackle that issue I simply used a lot of links to interconnect the related notes.
Then I had the problem of accessing these “Index” pages — Using search everytime to access them was annoying. To solve that, I put the index pages in Evernote shortcuts. Not only it allows me to access them quickly, I can even acccess them by keyboard — WIN+SHIFT+F (Open Evernote), CTRL+1 (Open first shortcut)