Just have to give a plug to:
Deluxe Town Diner
627 Mount Auburn Street
They have some of the best pancakes in beantown and I say this as someone who makes his own from scratch once a month or so!
The sourcream pancakes are out of this world as are the Ployes (a French Canadian speciality made from blonde buckwheat). They also do sweet potato which I have never tried.
Short stack, 2 big ones is $4.00 long stack $6.00.
Their hungry person breakfast for $10 or so is amazing (if you have not eaten in several days) it basically includes everything.
In general this place is pretty darn reliable; great meatloaf, etc., but they really shine for breakfast, pancakes in particular.
It is just about 6 blocks past the Cambridge line and near all of the Armenian stores.