Hi,
Although I work with EndNote X3, instead of X2 and Word 2007 instead of Pages '09, I think you should be able to do it this way:
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In EndNote, go to Edit > Output Styles > Open Style Manager…
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In this list, select the style you’re using (Numbered) and double-click it.
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Go to Citations, in that small menu you’ll find Template, click that.
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The default settings should look like this [Bibliography Number].
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You can now select that line, and change the font type and size and make it bold/italic/underlined.
I can’t see a way to change the colour though… (see the attachment image)
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When you’re done changing the template, go to File > Save, and save the style.
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Go back to Pages '09 and see if theres an option called ‘update citations and bibliography’, if that doesn’t show the changes instantly you can change the style to a different one and change it back to the ‘numbered’ style.
You should now be able to see the changes in your Pages '09 document (see attachment 2). Good luck!