Is there a bus that goes from Guadalajara to San Miguel De Allende? Can anyone give me an website where I could find out about the bus system in Mexico? Thanks!

I did a recent (less than two weeks ago) google and posted the threads on both Fodors and tripadvisor.com. for all the MX bus service web sites with schedules and fares.
M

There is a bus from almost anywhere to nearly anywhere in Mexico and, in most cases, excellent service. Just go to the bus terminal and get your ticket. I recommend first class service for a high degree of comfort and a fast trip. You will have no problem getting first class service from Guad to SMA.

The link is on Tripadvisor.com 18 July.
M

Yes, there is good connecting service. No, not many people use the internet in Mexico to buy tickets in advance. Most people just show up on the day of departure and buy a ticket for a seat on the next departing bus - or, in many cases, people buy a ticket a day in advance. Unless you're traveling during a special holiday period (i.e., Semana Santa or year-end) you'll find that there are seats available on just about any bus for just about each and every departure.