haha! I was just about to start I thread about this too! I have been look into this for a while now and I have been home sick so the past few days have allowed me to do a lot of research! Please know that this is only what I have researched, my idea of how it all works!
There are several different ways and organizations.
NCAA - 23 (maybe) schools, only girls allowed in Division 1, considered a varsity sport, most competitive, many rules about recruiting and competing - you may not earn money as a rider before/in college, each college may only hand out 15 scholarships for riding, must have advanced level of riding
IHSA - many more schools, largest organizations, welcomes all levels of riding, may hand out any number of scholarships, boys & girls allowed, does NOT have to be a team - can be a club*, has both western and english
*clubs are generally not sponsored by the school and you have to pay your own way, no scholarships are generally offered, coach has no say in recruiting, smaller, less competetive, more for fun
IDA - dressage only, offers scholarships, haven't researched as much so if anyone has info that would be great!
I have also found a great website. I suggest looking at it -http://www.equestriancollegerecruiter.com/
I would also make sure you look into how each program is run. I am currently a member of IEA (interscholastic equestrian association) and that has given me a lot of insight in to how college shows are run. I believe that all organizations have the same basic idea but they allow different warm-up times...i might be wrong...
Let me know if I can help and more. I will be interested in what everyone else says.