Yes - I remember what it was like. For a while I had so many exit and entry stamps in my passport every time I would enter or leave Schengen they would leaf through my passport then soon give up. Believe it or not, there is no one central system that keeps track of the days - it was up to the border guard to identify every stamp and count up the days. Maybe that will change with the new ESTA like system coming maybe next year. I remember once in Berlin I had a border guard that was young and clearly under supervision. He leafed through my passport then looked up at his supervisor with a worried look on his face, and the supervisor just waived me through.

The anecdotal evidence going around about overstays is you are more likely to get away with it (within reason) in southern Europe, but less likely in the more Germanic states. Once I received a stern lecture about not overstaying while leaving Zurich even though I was well within the 90 days (thanks to a detailed spreadsheet I was forced to keep). I'm sure he'll be fine and I believe the system is flexible enough to cater for flight delays etc.