Starting to plan this essay which I'm slightly dreading. My mind drifted and, a little frustrated by trying to annotate articles with bullet points, I came up with a JSON-based system.

An annotated article would look something like:

{
"citationKey": "Carreiras1996",
"tags": 
"summary": [
{
"summarySourceKey": "Reynolds2006"
"summarySourcePage": 94
"summaryText": "A summary of Carreiras1996"
}
],
"forMySubject": [
{
"page": 80
"quote": "This paragraph in Carreiras1996 supports my argument"
"note": "A personal note detailing how I'm going to integrate this into the essay"
"related": [
{
"relatedSupportKey": "Cole1994"
"relatedSupportPage": 900
"relatedSupportText": "We support Carreiras et al.!"
"relatedSupportNotes": "I should put this in the introduction."
},
{
"relatedAgainstKey": "Banaji1996"
"relatedAgainstPage": 1298
"relatedAgainstText": "Carreiras et al. are wrong."
"relatedAgainstNotes": "Don't mention this; hope the professor hasn't read the paper."
}
],
},
{
"page": 89
"quote": "This is another paragraph that supports my argument"
"note": "Yay, more evidence for my essay!"
}
],
"againstMySubject": [
{
"page": 81
"quote": "This paragraph in Carreiras1996 contradicts my argument"
"note": "A personal note detailing how I'm going to integrate this into the essay"
},
{
"page": 90
"quote": "This is another paragraph that doesn't support my argument"
"note": "Yay, more evidence for my essay!"
}
]
}

The essay plan would basically be various views of the data: either view by pro/con, or by language; key-specific text colour could be assigned based on the view chosen.

(Would this even work?)