I'm interested in going to grad school for a master's in computer science (I'm also applying to a MS/MBA program at a few schools). I have a 3.8 GPA from a highly regarded school, 99th percentile GRE scores, and not much else. I have no publications or research, minimal connections with professors, and my references will likely be only average. I do have some internship experience though. Should I bother?
I'm interested in going to grad school for a master's in computer science
There are two distinct types of masters degrees in computer science, at least in the US.
One is the professional masters degree, which is entirely course-based. Professional masters are considered terminal degrees; by pursuing such a degree you are cutting off (or at least drastically reducing) any future opportunity to join a PhD program. Also, professional masters students are rarely funded. You pay tuition, you take classes, you get your degree, and you leave, with a higher salary. High grades and test scores can definitely get you into these programs, even in top departments.
The other is the research masters degree, which requires some courses, but also includes a research component ending in a thesis. Research masters programs are often used as preparation for, or even soft entry into, PhD programs. Thanks to an explosion of undegraduate CS majors, it's become much more common for research masters students to be funded. Gaining admission to such a program, at least in top departments, usually requires more than just high grades and high test scores. You also need some evidence of research potential (which doesn't necessarily mean actual research experience).
First of all, you should know that GPA is mostly used as a negative factor. This means good GPA does not guarantee your spot in graduate school but bad GPA will definitely hurt your chance. GRE is the same but it has lower weight than GPA. In order to be accepted to top schools in US for PhD program you must have strong letter of recommendation and at least some quarters/semesters of research experiences. You mentioned you GPA but you did not specify what GPA you mean? is that your overall GPA or major GPA? regarding the question"Should I bother"? Yes. you should apply and you might have a good chance of being accepted to top schools in US for MS program since MS admission is handled different from PhD admission.
It is not clear what you want to do - research or industry. If the former, then you have no research experience in your degree program, which is a concern. You don't know if you like it, the grad school doesn't know if you like it or are at all good at it.. Maybe take a year and get a 'real job' while sorting this out. You can hire on at your school maybe as a tech, or as a saleried position for research programming type positions.
I am not sure you really need a MS to get into IT though, maybe you want to try the working world for a while before you change your mind?