Flew from Milan to London in February 05 and it was very tubulent as we were held at 27,000 feet - once we were given the ok to climb it was fine. Flew from Munich to Verona in September 06 and it was smooth. I think it depends on the weather, time of year, etc.
I have never found them too bad. That said, I nearly cancelled a trip recently from London to Bologna, Italy as a result of forecast (nasty) turbulence over the Alps. After much panicking, got on the plane and the flight was absolutely fine.
Travelling N to S or vice versa, the Alps are no more than 100 miles at the widest point, so even if there is turbulence, you'll be over them before you know it.
I was on a flight from Venice to Atlanta a couple Septembers ago. Flew right over the Alps and it was smooth as silk. In fact, the sky was spectacularly cloudless and you could see every detail of the landscape below, little farm villages nestled in between the valleys of the Alps. Never been on such a nice ride in my life. The flight didn't even start getting bumpy until we were way out in the middle of the Atlantic flying over a storm. Sometimes the clouds would part and I could look at the surface of the water 35,000 ft down and see all these white caps on the N. Atlantic, a sure sign of bad weather.