Get Monokai to work right with markdown. paste this into /Users/[your user name here]/Library/Application Support/Sublime Text 2/Packages/Color Scheme - Default/[YOUR_THEME].tmTheme

markdown.xml

<!-- copy this to YOUR_THEME.tmTheme-->
  <dict>
	    <key>name</key>
	    <string>diff: deleted</string>
	    <key>scope</key>
	    <string>markup.deleted</string>
	    <key>settings</key>
	    <dict>
	        <key>background</key>
	        <string>#EAE3CA</string>
	        <key>fontStyle</key>
	        <string></string>
	        <key>foreground</key>
	        <string>#D3201F</string>
	    </dict>
	</dict>
	<dict>
	    <key>name</key>
	    <string>diff: changed</string>
	    <key>scope</key>
	    <string>markup.changed</string>
	    <key>settings</key>
	    <dict>
	        <key>background</key>
	        <string>#EAE3CA</string>
	        <key>fontStyle</key>
	        <string></string>
	        <key>foreground</key>
	        <string>#BF3904</string>
	    </dict>
	</dict>
	<dict>
	    <key>name</key>
	    <string>diff: inserted</string>
	    <key>scope</key>
	    <string>markup.inserted</string>
	    <key>settings</key>
	    <dict>
	        <key>background</key>
	        <string>#EAE3CA</string>
	        <key>foreground</key>
	        <string>#219186</string>
	    </dict>
	</dict>

	<dict>
	    <key>name</key>
	    <string>Markdown: Raw</string>
	    <key>scope</key>
	    <string>text.html.markdown markup.raw.inline</string>
	    <key>settings</key>
	    <dict>
	        <key>foreground</key>
	        <string>#269186</string>
	    </dict>
	</dict>

	    <dict>
	        <key>name</key>
	        <string>Markup: Heading</string>
	        <key>scope</key>
	        <string>markup.heading</string>
	        <key>settings</key>
	        <dict>
	            <key>fontStyle</key>
	            <string>bold</string>
	            <key>foreground</key>
	            <string>#cb4b16</string>
	        </dict>
	    </dict>
	    <dict>
	        <key>name</key>
	        <string>Markup: Italic</string>
	        <key>scope</key>
	        <string>markup.italic</string>
	        <key>settings</key>
	        <dict>
	            <key>fontStyle</key>
	            <string>italic</string>
	            <key>foreground</key>
	            <string>#839496</string>
	        </dict>

	    </dict>
	    <dict>
	        <key>name</key>
	        <string>Markup: Bold</string>
	        <key>scope</key>
	        <string>markup.bold</string>
	        <key>settings</key>
	        <dict>
	            <key>fontStyle</key>
	            <string>bold</string>
	            <key>foreground</key>
	            <string>#586e75</string>
	        </dict>
	    </dict>
	    <dict>
	        <key>name</key>
	        <string>Markup: Underline</string>
	        <key>scope</key>
	        <string>markup.underline</string>
	        <key>settings</key>
	        <dict>
	            <key>fontStyle</key>
	            <string>underline</string>
	            <key>foreground</key>
	            <string>#839496</string>
	        </dict>
	    </dict>
	    <dict>
	        <key>name</key>
	        <string>Markup: Quote</string>
	        <key>scope</key>
	        <string>markup.quote</string>
	        <key>settings</key>
	        <dict>
	            <key>fontStyle</key>
	            <string>italic</string>
	            <key>foreground</key>
	            <string>#268bd2</string>
	        </dict>
	    </dict>
	    <dict>
	        <key>name</key>
	        <string>Markup: List</string>
	        <key>scope</key>
	        <string>markup.list</string>
	        <key>settings</key>
	        <dict>
	            <key>foreground</key>
	            <string>#657b83</string>
	        </dict>
	    </dict>
	    <dict>
	        <key>name</key>
	        <string>Markup: Raw</string>
	        <key>scope</key>
	        <string>markup.raw</string>
	        <key>settings</key>
	        <dict>
	            <key>foreground</key>
	            <string>#b58900</string>
	        </dict>
	    </dict>
	    <dict>
	        <key>name</key>
	        <string>Markup: Separator</string>
	        <key>scope</key>
	        <string>meta.separator</string>
	        <key>settings</key>
	        <dict>
	            <key>background</key>
	            <string>#eee8d5</string>
	            <key>fontStyle</key>
	            <string>bold</string>
	            <key>foreground</key>
	            <string>#268bd2</string>
	        </dict>
	    </dict>