I'm not sure if anyone at Evernote has taken note of LiquidText, but if not, you really should check them out. There is one feature they have that I'm desperate for and one other which is quite neat.
1. Notes on notes
I make notes from books and online articles mostly. Oftentimes I want to make a "note on that note", like "I disagree with this, here's why", "this is contentious, here's why". But at the moment, I have to either 1) make those observations in a separate note and then link to that note, which creates "false positive" search matches, or 2) make the observations within the