This script will (as the title suggests) export all of you Skim notes to a text editor (either TextEdit or TextMate) in Markdown format, with reference style links. It relies on the GENERATE TOP 3 NOTES WITH SYSTEM URL script that will put 3 notes at the top of the PDF with linking information.

Export All Skim Notes with Markdown Reference Links

(* EXPORT ALL SKIM NOTES TO A TEXTEDITOR WITH MARKDOWN REFERENCE LINKS

-- Stephen Margheim
-- 16 July 2013
-- open source

This script will (as the title suggests) export all of you Skim notes to a text editor (either TextEdit or TextMate) in Markdown format, with reference style links. It relies on the GENERATE TOP 3 NOTES WITH SYSTEM URL script that will put 3 notes at the top of the PDF with linking information. 
To change which text editor it exports to, change the "theEditor" property. It can be either "TextMate" or "TextEdit". 

When launched, the script will ask you if the current PDF is a Primary Source or a Secondary Source. Your choice will determine the text values for the 6 different highlight colors. Of course, you can change any and/or all of the text values to what you wish.  
*)



(* PROPERTIES *)
property LF : (ASCII character 10)
property LF1 : (ASCII character 32) & (ASCII character 32) & (ASCII character 10)
property tid : AppleScript's text item delimiters

--if you use TextMate, change this property to "TextMate" and be sure you have an open, empty TextMate file
property theEditor : "TextMate"


(* THE SCRIPT *)
tell application "Skim"
  set theTextStatus to display dialog "Is the PDF a Primary or Secondary text?" buttons {"Primary", "Secondary"} default button {"Secondary"}
	
	--get info for all notes
	set allNotes to every note of document 1
	set allNotes_types to every type of notes of document 1
	set allNotes_text to text of every note of document 1
	set allNotes_pages to index of every page of every note of document 1
	
	--get info for all notes except top 3
	set selNotes to items 4 through -1 of allNotes
	set selNotes_types to items 4 through -1 of allNotes_types
	set selNotes_text to items 4 through -1 of allNotes_text
	set selNotes_pages to items 4 through -1 of allNotes_pages
	
	--get info from those top 3 notes
	set Markdownlink to (get text of note 2 of page 1 of document 1) as string
	set pdfTitle to (get extended text of note 1 of page 1 of document 1) as string
	set PDFLink to (get text of note 1 of page 1 of document 1) as string
	set number_of_Note3 to (get text of note 3 of page 1 of document 1) as string
	
	--prepare Headers for all of the various note types
	set notesText_text to "- - -" & LF & LF & "## The ToC ##" & LF1 & LF & LF
	set notesText_anchor to "- - -" & LF & LF & "## All of my Text Notes ##" & LF1 & LF & LF
	set notesText_highlight to "- - -" & LF & LF & "## All of the Highlighted Text ##" & LF1 & LF & LF
	set notesText_underline to "- - -" & LF & LF & "## All of the Underlined Text ##" & LF1 & LF & LF
	set notesText_strikethru to "- - -" & LF & LF & "## All of the Strike-Through Text ##" & LF1 & LF & LF
	set FinalText to "# Notes: " & pdfTitle & LF1 & "= PDF Notes" & LF1 & "@ notes" & LF1 & LF & LF
	
	
	(* THE MEAT-N-POTATOES OF THE SCRIPT *)
	repeat with i from 1 to count of selNotes_types
		
		--prepare Skim page # and actual page #
		set notePage to item i of selNotes_pages
		set theRealPage to notePage + number_of_Note3 as string
		
		--collect Text Notes
		if item i of selNotes_types is text note then
			set noteText to item i of selNotes_text
			set LinkID to my randomize("1")
			
			set notesText_text to notesText_text & noteText & " ([p." & theRealPage & "][" & LinkID & "])" & LF1 & LF & "[" & LinkID & "]: " & PDFLink & notePage & LF & LF
			
			--collect Anchor Notes	
		else if item i of selNotes_types is anchored note then
			set titleText to item i of selNotes_text
			set noteText to extended text of item i of selNotes
			set LinkID to my randomize("2")
			
			set notesText_anchor to notesText_anchor & "**" & titleText & ":** " & noteText & " ([p." & theRealPage & "][" & LinkID & "])" & LF1 & LF & "[" & LinkID & "]: " & PDFLink & notePage & LF & LF
			
			--collect Underline Notes	
		else if item i of selNotes_types is underline note then
			set noteText to item i of selNotes_text
			set LinkID to my randomize("3")
			
			set notesText_underline to notesText_underline & "\"" & noteText & "\"" & " ([p." & theRealPage & "][" & LinkID & "])" & LF1 & LF & "[" & LinkID & "]: " & PDFLink & notePage & LF & LF
			
			--collect Strike-Thru Notes	
		else if item i of selNotes_types is strike out note then
			set noteText to item i of selNotes_text
			set LinkID to my randomize("4")
			
			set notesText_strikethru to notesText_strikethru & "\"" & noteText & "\"" & " ([p." & theRealPage & "][" & LinkID & "])" & LF1 & LF & "[" & LinkID & "]: " & PDFLink & notePage & LF & LF
			
			--collect Highlight Notes	
		else if item i of selNotes_types is highlight note then
			set theColor to color of item i of selNotes
			set titleText to my color2text(theColor, theTextStatus)
			set noteText to item i of selNotes_text
			set LinkID to my randomize("5")
			
			set notesText_highlight to notesText_highlight & "**" & titleText & ":**  " & LF1 & "\"" & noteText & "\"" & " ([p." & theRealPage & "][" & LinkID & "])" & LF1 & LF & "[" & LinkID & "]: " & PDFLink & notePage & LF & LF
		end if
	end repeat
	
	--extract only the "Summary" highlight notes
	set theSummary to {}
	set theParas to paragraphs of notesText_highlight
	repeat with i from 1 to count of theParas
		if item i of theParas contains "**Summary" then
			set theTitle to item i of theParas
			set theText to item (i + 1) of theParas
			set theRef to item (i + 3) of theParas
			set theSumm to theTitle & LF & theText & LF & LF & theRef & LF & LF
			copy theSumm to the end of theSummary
		end if
	end repeat
	
	--remove "Summary" highlight notes from collection of highlight notes
	if (not (theSummary is {})) then
		set SumText to theSummary as string
		set SumList to paragraphs of SumText
		set empty to {""}
		set FinalSum to my cleanmyList(SumList, empty)
		
		set HighList to paragraphs of notesText_highlight
		set finalHighlights to my cleanmyList(HighList, FinalSum)
		set AppleScript's text item delimiters to LF
		set notesText_highlight to (finalHighlights as string)
		set theSummary to "- - -" & LF & LF & "## Text Summary ##" & LF1 & LF & LF & SumText
	end if
	--ALWAYS RETURN TEXT ITEM DELIMITERS TO NORMAL
	set AppleScript's text item delimiters to tid
	
	--remove any note sections that are empty
	set FinalList to my textCheck(notesText_text, notesText_anchor, notesText_highlight, notesText_underline, notesText_strikethru, theSummary)
	
	--prepare the final collection of notes, with MetaData
	set FinalText to FinalText & FinalList
	
	--export to pre-determined text editor
	if theEditor is "TextEdit" then
		tell application "TextEdit"
			activate
			set newDoc to make new document with properties {text:FinalText}
		end tell
		
	else if theEditor is "TextMate" then
		tell application "TextMate"
			insert FinalText
		end tell
	end if
	
end tell









(* HANDLERS *)

--convert highlights into text values
on color2text(noteColor, theTextStatus)
	set colorText to {}
	
	if theTextStatus is {button returned:"Secondary"} then
		if noteColor is {64634, 900, 1905, 65535} then
			set end of colorText to "Disagree"
		else if noteColor is {64907, 32785, 2154, 65535} then
			set end of colorText to "Agree"
		else if noteColor is {65535, 65531, 2689, 65535} then
			set end of colorText to "Summary"
		else if noteColor is {8608, 65514, 1753, 65535} then
			set end of colorText to "Reference"
		else if noteColor is {8372, 65519, 65472, 65535} then
			set end of colorText to "Quotable"
		else if noteColor is {64587, 1044, 65481, 65535} then
			set end of colorText to "Technique"
		end if
		
	else if theTextStatus is {button returned:"Primary"} then
		if noteColor is {64634, 900, 1905, 65535} then
			set end of colorText to "Key Quote"
		else if noteColor is {64907, 32785, 2154, 65535} then
			set end of colorText to "Key Theme"
		else if noteColor is {65535, 65531, 2689, 65535} then
			set end of colorText to "Summary Passage"
		else if noteColor is {8608, 65514, 1753, 65535} then
			set end of colorText to "Key Motif"
		else if noteColor is {8372, 65519, 65472, 65535} then
			set end of colorText to "Confusing Passage"
		else if noteColor is {64587, 1044, 65481, 65535} then
			set end of colorText to "\"Purple\" Passage"
		end if
	end if
	return colorText
end color2text


--generate random link IDs
on randomize(theVal)
	set theAlphabet to {"a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z"}
	set randomLetter to random number from 1 to 26
	set randomLetter to item randomLetter of theAlphabet
	set theNum1 to random number from 1 to 9
	set theNum2 to random number from 1 to 9
	set LinkID to theVal & theNum1 & theNum2 & randomLetter
	return LinkID
end randomize

--remove any empty note sections
on textCheck(notesText_text, notesText_anchor, notesText_highlight, notesText_underline, notesText_strikethru, theSummary)
	
	if notesText_text is "- - -

## The ToC ##  


" then
		set notesText_text to ""
	else
		set notesText_text to notesText_text & LF & LF
	end if
	
	if notesText_anchor is "- - -

## All of my Text Notes ##  


" then
		set notesText_anchor to ""
	else
		set notesText_anchor to notesText_anchor & LF & LF
	end if
	
	if notesText_highlight is "- - -

## All of the Highlighted Text ##  


" then
		set notesText_highlight to ""
	else
		set notesText_highlight to notesText_highlight & LF & LF
	end if
	
	if notesText_underline is "- - -

## All of the Underlined Text ##  


" then
		set notesText_underline to ""
	else
		set notesText_underline to notesText_underline & LF & LF
	end if
	
	if notesText_strikethru is "- - -

## All of the Strike-Through Text ##  


" then
		set notesText_strikethru to ""
	else
		set notesText_strikethru to notesText_strikethru & LF & LF
	end if
	
	if theSummary is {} then
		set theSummary to ""
	else
		set theSummary to theSummary & LF & LF
	end if
	
	return notesText_text & theSummary & notesText_anchor & notesText_highlight & notesText_underline & notesText_strikethru
end textCheck

--remove items from a list
on cleanmyList(theList, itemsToDelete)
	set cleanList to {}
	repeat with i from 1 to count theList
		if {theList's item i} is not in itemsToDelete then set cleanList's end to theList's item i
	end repeat
	return cleanList
end cleanmyList

Not working. Strange. http://i.imgur.com/rtPLvQJ.png