Chris has a great response (^).
I'll add that different pickups drive the front end of your amp differently. If you want a great vintage Les Paul tone then you're not going to want to use the Gibson 469R/500T pickup set in your Les Paul because they're too hot.
Also, different pickup magnets give different responses. Alnico II, III, IV, V, VIII, ceramic, etc all give different frequencies. Swapping magnets in the same pickup will make it sound like a different pickup.
I've bought 13 or 14 pickups and swapped them in various guitars. Some of them replaced the "Duncan Designed" pickups with real Seymour Duncans and I found it made a positive difference in the tone. I also installed the EMG 81/85 Zakk Wylde set in my Schecter because I wanted more of that metal tone than the stock Duncan Designed.
Different pickups for different applications.
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