M2 is a term used to refer to Misha Collins and Mark Pellegrino. It can simply be used as a shorthand term for the actors, or specifically in real person slash to indicate the pairing Misha Collins/Mark Pellegrino. The shorthand came into use following the Asylum Europe: No Rest for the Wicked 2010 convention at which the two actors shared a panel to great success.
Jumping in to say that the only time I've ever heard the designation M2 it has been in regards to Misha Collins and Mark Sheppard.
See also: Marksha
More information: Real Person Slash