A great ramen place to try is in Ebisu. I think it's called 99 ramen (or quew jew quew).  To get there, exit Ebisu station through the West exit and then walk to the main road and turn right back under the train tracks.  Continue down that road a couple of blocks until you get to a street that has a pedestrian bridge.  Cross the bridge and continue down the road just a few stores.  You can't miss it as it is always busy. (map)

They have cheese ramen.  Although it's interesting I don't recommend you order it as a main meal.  It's like eating a big bowl of cheese.  The rest of their ramen is great.