How does one change to engineering for graduate school after undergrad in a science field? I've always had an interest in electrical engineering (actually all engineering in general) and I've decided that I'd like to pursue a graduate degree.  I guess I'm wondering if I should really try to do this or just keep it as a fun hobby I spend all my free time doing.

So, the question is,  how does one change fields between undergrad and grad school?  A specific example follows, but please provide answers that address a more general case, so that your answers will be helpful to other people with the same general question.

I already have a BS and MS in chemistry with a minor in applied math.I published three papers during my MS, one first author in the top journal in my specialty and two as coauthor in an average and a so-so journal.  I hope those will count for something.  I finished my BS with around 3.1 and my MS with a 3.9 gpa.  I'm sure that my MS advisor would write me a great letter.  My GRE scores are too old to count so I'd have to retake it or try and get a pass on it since I already have a graduate degree.  Since finishing school I've been working for 4 years as a chemist.  I can get great recommendations from my supervisor who is a PhD chemist.    

I've been working for a while to cover some of the things I would have learned in a BSEE to try and make up for my lack of one.  I worked through some texts on analog/digital design, lots and lots of programming, built a balancing robot that got a bit of internet attention, and I'm currently working on an autonomous robotics project that's looking really good so far.  After that I have more project ideas than I have time or money for.  

I want to apply for PhD programs (specifically in controls/robotics) but I'm worried that my application will get tossed right away because I don't have a BSEE.  Maybe I should just apply to MS programs?
I will answer a slightly more general question.  How does one change fields between undergrad and grad school?  The answer very carefully is correct, albeit unhelpful.  The single most important criteria when applying for a strong PhD (at least in math, engineering, or the natural sciences, but probably true in other fields too) are letters of recommendation and demonstrated research ability.  Bad grades can sink your application, but good grades (even from a top school) are not enough to get you in (nor good test scores, although they help).  

If you want to get a PhD, but don't have any experience in the area, you should first apply to a masters program, where you can gain experience and impress potential letter of recommendation writers.  Often admission to a masters program is less competitive than to a PhD program (if even getting into the masters program is difficult, you could start as a non-degree student).  But if you can publish a few papers during your masters and convince a few of your professors that you have both the ability and desire to succeed in grad school, then you're application to a PhD program will be much stronger.  I also recommend that you talk with the schools where you plan to apply and ask what they suggest that you do to strengthen your application.

You might also like to read this question and answer Is it possible to attend graduate school in pure math after undergrad in CSE?