Does it look bad if letter of recommendation comes from an emeritus professor? I wonder is it a good idea to ask for a letter of recommendation from a emeritus professor who I took his course and knows me well? 

I was wondering is it bad to get a letter from someone who is not in Academia anymore?
The best reference is the one that is both honest and based on extensive firsthand knowledge of your qualities. Emeritus status would seem irrelevant to me.