Computer Science - It is the standard "programming major". It has been around and defined for ages. When someone hires a computer scientist, they can expect them to know C/C++ or Java or both and most likely other languages. People know what it is and will understand your background without much explaination. You can get a Masters in Computer Science.
Software Engineering - a new breed of programming major. Not all major schools even offer it. No one is really sure what it means or how it differs from CS other than the people teaching it and the schools offering it. Major companies will be confused by it and they will ask you what sort of classes you took. Several schools don't even have an accredited program for it since it hasn't been around long enough for someone to graduate from those schools with the degree.
In short, I'm not even sure what Software Engineering is, but I think it's a crappy attempt for people to call themselves "engineers" when they're just programmers. Is there engineering in programming? Maybe.... but if you're strictly programming based off of proven models, I don't think there is much engineering going into it.
That's my take on it anyways. I'm sure someone will refute it because I think there are a few people here taking Software Engineering.
EDIT: Further reading... and there are some good articles there.
EDIT 2: Apparently I forgot to post the link, or the board decided to remove it. http://www.google.com/search?q=compu...utf-8&oe=utf-8
