Two years ago, I switched to using Evernote and just recently back to pen and paper. The two big issues that I had with Evernote where:
(1) It didn't really support a nice view for code snippets & diagrams
(2) I don't really want to store my notes "forever"
To me, notes are ephemeral. I want to hold on to them only as long as I need them and then either toss them or copy them into a more formal document structure.
These days, I keep all my notes on a legal pad as just one running disorganize scroll. Once a week, I go through the pad, tear out all of the pages that I wrote on. Then I copy all of the notes that I still need on to a clean sheet of paper and toss the old ones. The copying process helps me to review the notes and internalize them.
If notes are really important enough that I need to keep them long-term. Then I type them up into a nice LaTeX document, convert it to a pdf and print it out. Then inevitably end up writing all over the print out.
I don't think an application could be made to make me switch. The mechanical process of hand writing helps with memory and couldn't be replicated with a computer environment. As for my document store. I prefer everything to be in plaintext on my system where I can automate a lot of my interaction with the documents. If anything, I would like an easier method for asset management -- I take pictures with my phone of my hand drawn diagrams to include as illustrations in my documents. The process of take a picture, get it on my linux box, clip the photo to the relevant section, put it in an asset directory, and link to it still has too many steps. But I'm hoping to automate that myself one of these days.
Just as an aside. It seems like a lot of note-taking applications keep focusing on team-note-taking. Which doesn't do anything for me. I take notes for myself. They are often rude, crude, and full of shorthand jibberish that I don't expect team mates to ever understand more or less look at.