Basically, pups are eq-ed for either the neck or bridge.
Since at the bridge, the tones are generally brighter and more harmonically responsive, plus clearer and thinner sounding... the bridge pups tend to less bright (to knock off the brightness) and thicker sounding. Of course, there are bridge pups that do otherwise but this is the general idea.
The neck area has a "looser" tone... not as tight as the bridge, less harmonically responsive and thicker sounding. Plus its darker there. Neck pups tend to focus on clarity and brightness.
You can imagine if you put a bright, hot bridge pup in the neck... its going to sound difference definately. Some like it, some don't... up to you.