What proportion of planetary systems have been found with 'Hot Jupiters'
In 2011, about 20% of the exoplanets found were hot Jupiters. That is a lot, but it is strongly biased simply because there are the easiest planets to detect. You can detect exoplanets by transit (that means that the planet passes in front of its host star which decreases the luminosity of the observed star during the transit), hot Jupiters being closer to their host star and bigger than smaller planets will therefore be easier to detect. You can detect exoplanets by radial velocity, which means that you detect variation of the position of the host star due to planet's gravity. The closer and the heavier the planet is, the larger the variation will be, and therefore the easier to detect.

That's why it is important to say "In 2011"; as our detection techniques (and telescopes) improve, the proportion of hot Jupiters should decreases.

Edit:
To put that in perspective, you can read this article from Jason Wright in which he tries to estimate the "real" ratio of hot Jupiters orbiting around "normal" stars (F, G and K type stars). This ratio is actually much smaller than the currently observed ratio, about 1.2%.