I had a really hard time with this because my friends and doctor told me to wake him if he was going over schedule. Basically, your goal is to get your baby to sleep through the night. This is gradual, so you are trying to eliminate feedings slowly. But during the day, it is suggested that you feed your baby every 3 to 4 hours AND that you get 6 feedings in during the day. Well, my son always slept past this mark. So, I had to wake him A LOT. I would go in and stare at him, chicken out and run out and call my husband. I usually forced myself at the 4.5 hour mark after I would envision being up in the night an extra time.
So, I say, definitely wake a sleeping baby but only until about 4 months. This is advice I got from the book Baby Whisperer. I noticed that I didn't generally have to wake him as much around 3 months or 3.5 months. And by 4 months, he was on a pretty decent routine. But, there were maybe 2 times where I woke him after 4 months, and it was very hard for him to get up and he was fussy. When they are newborns, babies can sleep anywhere, eat anytime, etc. But as their internal clocks start to form, it gets harder to break up their routine.
And you'll notice that baby won't be able to sleep on the run anymore. You will be stuck at home while he sleeps in his cozy crib. But it is worth it to have a happy, rested baby!