A University is a collection of colleges. Often colleges have a focus in an area. Several areas brought together can be a University. If the institution is not so organized or large as to have the title University, it will be a college.
As a student, there may not be a large difference. Your degree (aside from reputations of specific schools) will have the same function in the end. Great (and not so great) teachers, courses and programs are found at both. While choosing a school, I recommend looking at both styles,
Choose based on the people and faculty you meet while visiting (specifically the ones you will work under). Also consider the program and classes you can read about or ask about (does it fit your interests). Of course, another consideration is the price and location- if these things are an issue to you. These are the important things. You may also talk with people who have graduated from the schools you are considering... How are they doing in the job market? Do they find the school reputable? Did they benefit from the education in other ways also? Do not worry about the title of the school as much.