I think most of these 'advanced' note taking features (even interlinking when used pervasively) distract more than it helps.

> Regular note taking sucks

It sucks the least, I tried some of note taking apps and software, then settled at some lines of shell script.

    notes () {
        cd ~/notes/$1
        clear
        ls
    }

    note () {
        vim $@
        clear
        ls
    }

This works surprisingly well for most purposes, along with syntax highlighting for markdown. I sometimes wish it had interlinking and images, but I haven't come across a situation where I needed it.