difference pickups can make in the tone of your guitar. I always thought it was only really the amp that made the difference. I'm sure lots of people dont like certain amps and i bet if they just changed their pickups they would realize their amp isnt all that bad. I have heard about some pickups sounding very similar on any guitar and other pickups having a very different tone depending on the actual guitar.
The strings can have a difference in tone...

thicker strings will make your tone sound more heavy and add more bass to it. Thicker strings also give you more sustain. They will produce more volume too.
There are also bad things about thicker strings which effect your the playability of the guitar which you probably know about anyway.
The wood will have a slight effect. Guitars designed for lead players and rythem players will be made of different wood. I dont know which type of wood is used for what though. I think the type wood may effect how some pickups work too.

etc etc .... i dont know what i'm on about.

Hope this all helps ;)

(dont you hate it when you just finish writing something and you accidently delete the last paragraph.. well that just happend to me)