Getting Greek characters to display properly in a PDF generated from Markdown with Pandoc has caused some frustration today - here's what eventually worked for me:
Use xelatex instead of pdflatex:
pandoc --pdf-engine=xelatex
Use Linux Liberatine O as the font in your Markdown metadata:
mainfont: "Linux Libertine O"
I'm a bit sad that I can't use Palatino, which I think is a nicer font, but Linux Libertine 'just worked' and is free (as in beer and speech).
