Breadth of study typically. As was stated, self taught programmers tend to have a narrow focus, not a guarantee to be avoided in college but perhaps less common in a good program. It depends on how thoroughly self taught you are, and that's at least what a degree is supposed to say. A student is at least _this_ educated. Depends on the reputation of the school. Of course, any self-taught programmer worth his salt can probably impress an employer in an interview just as well if not better than a student, but I think it's easier to get a leg up on the job market out of college than out of high school, if you didn't already have an 'in' to the industry.
There's probably a lot of self-taught developers out there who aren't familiar with things like Scrum, agile development, pair programming, code refactoring, ORM, MVC, etc. But I'm sure there's some that are, so like I said it depends on the quality of your own education. You can't get a degree at my school without at least a minimal exposure to those however, and some classes require utilization of some of those practices in the capstone or other high level team development courses. Self-taught programmers are also, from my experience, less likely to have spent much time working in teams, but again that's not always the case.
My friend Andrew though is an amazing sys admin, who can also code very capably, and never went to college. There's a few industry-type subjects I know a bit about that he hasn't been exposed to but by and large he's a hell of an employee. He's probably going to work for Facebook in the near future. But he didn't work on a team of devs until 6 months ago, and he's 26 years old now, been working for the last 8. He was always a one man show, doing sys admin, web development, the whole works for small companies. But he's been doing great on a team too. A lot of your lone coders aren't like that.