Send color-coded Skim.app PDF notes to the clipboard with custom page urls. (See http://drosophiliac.com/2012/09/an-academic-notetaking-workflow.html)

Skim_notes_to_clipboard.scpt

tell application "Skim"
  set the clipboard to ""
	set numberOfPages to count pages of document 1
	
	activate
	set myColorCodes to my chooseColor()
	
	set firstPage to "1" as number
	set lastPage to numberOfPages
	set the clipboard to "# Notes" & return & return
	
	repeat with currentPage from firstPage to lastPage
		set pageNotes to notes of page currentPage of document 1
		exportPageNotes(pageNotes, currentPage, myColorCodes) of me
	end repeat
	
end tell

on exportPageNotes(listOfNotes, pageForProcessing, myColorCodes)
	tell application "Skim"
		
		set currentPDFpage to pageForProcessing
		repeat with coloredNote in listOfNotes
			
			repeat with i from 1 to the count of myColorCodes
				if color of coloredNote is item i of myColorCodes then
					set categoryColors to ({"Summary", "Technique", "Result", "Reference", "Hypothesis", "Question or connection"})
					set noteColor to color of coloredNote as string
					if noteColor is item i of myColorCodes as string then
						set noteColor to item i of categoryColors
					end if
					set noteText to get text for coloredNote
					set the clipboard to (the clipboard) & "**[" & noteColor & "]" & "(skimmer://" & name of document 1 & "#page=" & pageForProcessing & ")**" & ":   " & return & noteText & return & return
				end if
			end repeat
		end repeat
		
	end tell
end exportPageNotes

on chooseColor()
	set selectedColors to ({"Summary", "Technique", "Result", "Reference", "Hypothesis", "Question or connection"})
	set colorCodes to {}
	set noteColor to ""
	repeat with noteCol in selectedColors
		set noteColor to noteCol as text
		if noteColor is "Summary" then
			set end of colorCodes to {64634, 900, 1905, 65535}
		else if noteColor is "Technique" then
			set end of colorCodes to {64907, 32785, 2154, 65535}
		else if noteColor is "Result" then
			set end of colorCodes to {65535, 65531, 2689, 65535}
		else if noteColor is "Reference" then
			set end of colorCodes to {8608, 65514, 1753, 65535}
		else if noteColor is "Hypothesis" then
			set end of colorCodes to {8372, 65519, 65472, 65535}
		else if noteColor is "Question or connection" then
			set end of colorCodes to {64587, 1044, 65481, 65535}
			
		end if
	end repeat
	
	return colorCodes
end chooseColor