We rarely run as punishment, although it is used occasionally. We try and develop the mindset the "winners run," and using it as punishment can take away from that.
Our most effective tool is a "work crew" duty, where kids perform some type of manual labor around the field. This is most effective when they have to do it on Fridays when we have coach pitch scrimmages.
John Wooden said that the most effective tool for punishment is the bench. In the offseason that is difficult, but we've found this works well. What every kid wants is to play, so taking that away from them is key. Some don't mind running, as long as they get to play.
Again, I'm not against running everyone sometimes, it can be very effective. But over time will lose it's impact if that's all you do.