Sorry if this is a stupid question, but what is the difference between them? What are the advantages/disadvantages. I'm looking to replace my factory Bose speakers and I wanted to know what type of speakers I should get for the front and the back to go with a 12" sub.

 

2 way speakers have 2 speakers in it. Kinda like a tweeter and a woofer.
3 way speakers have 3 speakers in it. I think its like a tweeter, mid-range, and woofer

 

What about components? And what do most people get for the front door and rear deck speakers to go with subs?

 

Components are the same thing but the speakers are separate pieces. Usually you use components for the front speakers so you can mount the tweaters up high and the woofers in the door panels. In the rear you just want fill, so use a two-way; some people even say not to use any tweeter at all in the rear, just a woofer. Either way, you don't want the tweeters to be too loud in the rear or the music will sound like it's coming from behind you.

Since you're obviously a car audio noob, here's a good faq for you to browse: http://www.mobileaudio.com/rac-faq/