I own a 996 from 1999, have done since 2001. When I bought it, all my mates said "ooh, Ducatis... unreliable....."
In that time I have been trailered home twice (once after a puncture, once after I threw it down the road) and stranded (at a pub, fortunately) once, when the immobiliser, er, immobilised...
I had more trouble with my old zx6r than I ever did with the 996. It's just a myth that they're unreliable.
Mind, mine hasn't been out of the garage in 18 months so it hasn't had much chance to break down recently