Do I have a better chance for a PhD in a field I have research experience in or one I have had better courses on? I'm applying for PhD programs in Computer Science, which allow a year of rotation and courses, before the student officially joins a lab for their thesis. I've had research experience in Computational Biology, but being a Math major, I've had a relatively (relative to average CS graduates) large number of courses on (or related to) Theory CS (I took quite a few advanced courses on topics closely related to Theory CS). 

I have two questions:

1 - Do admissions committee generally view an applicant in my situation more qualified for doing a PhD in Theory, or in Comp bio?

2 - Assuming I'm considered more qualified for Comp Bio, is it a bad idea to express interest in working in CompBio, and claim I want to work with an advisor in that area, while I actually plan to do my PhD in TCS? I mean, given that once I get in I'll have the freedom to choose my advisor and I'll have enough time and opportunities to even gain research experience in a different area, could there be any negative consequences in expressing interest in CompBio (and even introduce some vague research ideas), and then if admitted, try to work on TCS? 
(moral issues with doing this are of course a different story)
Apply for and do the PhD you actually want to do. 

The skills gained by having research experience are generally subject transferable, so if you want to do theoretical computer science, explain what skills and knowledge your research experience in computational biology gave you that would be applicable to that field. It could even be something as simple as saying "my experience in researching x topic in computational biology got me interested in computer science as a field of research, which I want to explore further, focusing on theoretical topic y".

Don't try and game the system. Be honest about your interests and the experiences that have led you to them.