I did a CE degree (Computer Systems Engineering) at Stanford. To be honest, I should have listened to my CS advisor, who said CE really doesn't give you enough depth in either CS or EE. Four years pass fast, and invariably a CE degree is the "no theory" or "less theory" degree. This will hurt you in the long run if you end up choosing CS or EE as your eventual interest. Lacking a strong algorithms / theory background, it can hurt both when interviewing (most great programming shops place a heavy emphasis on running times and algorithms) and when actually developing code. On the EE side, you pretty much need a PhD or at least a MS to get one of the more interesting R&D positions. And for applying to grad school, you'll be up to your more solidly EE brethren who have that much more coverage of the material and connection with EE faculty.

My suggestion: try some of both, and make a decision, and go deep.

If your college really is a 'java school' -- consider doing well your freshman year and transferring to a school known for solid CS instruction. It'll probably make a difference.

Good luck!

Thanks, this helps a lot, I'm leaning towards CS. Does anybody else have any advice?

I am about to complete my CE degree. I chose the program because 1. my school has a weak CS program (which is part of the business dept.) and 2. I was already familiar with programming out of high school, so I wanted to get some hardware experience. I have found CE to be a nice middle ground between CS and EE, with an emphasis on engineering principles that you probably wouldn't find in a CS program. I also learned a lot more math than I would have otherwise. If you find your CE program lacking in theory, you can always take a few elective courses.

As a Bachelors degree, I think CE is a great compromise between CS and EE. I don't believe you would have any trouble pursuing a graduate degree in CS or EE, given that choice.