Race replica sportbikes come in these standard engine sizes/flavors, as a general rule (Ducati an example of exception). This is very often the basis for those numbers.
250 cubic centimeters (cc)
1000 cc (aka "liter" bike)
Within a particular brand and line (like the Suzuki GSX-R) it is reasonable to say the higher the number the more horsepower it can create. However, you cannot make such comparisons across different types of engines because they create power in different ways and are thus suited to particular uses. Engine types include inline 4's (GSX-Rs use these), V-4s, triples, boxer twins... This looks like a good reference to the configurations, and Wikipedia has some nice info too.
Please keep in mind that comparing an engine size of supersport to a Harley is a major mistake. Sportbikes are vastly more powerful than Harleys with a similar engine size in almost all cases.
Dragging knee is for the track, and dragging tail is for the lot. --Kane Friesen
When you're in a car, you're watching a movie; when you're on a bike, you're in the movie. --Robert Pirsig