As an undergrad, I was a double-major in neuroscience and music. Now, I'm working on putting together a CV for applications to master's programs in neuroscience. But, my thesis work was done in the music department and unrelated to neuroscience whatsoever. Should I include this on my CV, or would it be seen as irrelevant "padding" of my CV? (I'm not really concerned about shoring up my experience, as I've had several years of directly relevant work experience since I finished my bachelor's degree.)
If your undergraduate program requires a Bachelor's Thesis, graduate school admissions committees might expect to see it on your CV. Completely omitting your thesis in your CV might raise questions.
Your ability to do independent work is also important, even in another field. If your thesis work is not related to your graduate school field, I would mention it but not focus on it. (i.e., include the title and one sentence summarizing what you did). If your Bachelor's Thesis is publicly accessible (and it is a good thesis), citing it in your CV cannot hurt.
As a past admissions committee member for graduate studies (in a different discipline), one of our biggest concerns were which applicants had the independence, stick-with-it-ness, and structuring and writing ability to finish a degree. A thesis in any discipline is solid evidence of that and will likely be looked on favorably.
From another angle, it is worth noting that academia favours CVs - which stands for curriculum vitae, the course of one's life. These tend to be multipage documents including all accomplishments concievably of relevance to the reader. Of course, a CV should be tailored to the audience, but basically you include everything and the bar for calling something "padding" is pretty high (low?). This is very much in contrast with industry-favored résumés, highly selective summaries chosen to be most directly applicable to the position being sought. That's why résumés tend to be 1-2 pages even for an accomplished experienced professional, while even a pretty junior CV is likely to be much longer.
Put it in for clarity, it's not padding. The point of a CV is not just to claim a set of knowledge, but to provide evidence of skills like research, analysis, self-motivation.
Also, you never know where you are going to end up, some time in the future you may do research at the intersection of these interests (such as how the brain interprets music).
There are two key elements of such applications, normally called the CV and the SoP (Statement of Purpose). Your CV details your past accomplishments and should probably be complete. Your SoP is directed at your future goals with some care given as to how the past enables the future.
So, my recommendation is to include everything in the CV. This avoids any possible future problem of anyone thinking that there are gaps and wondering why you are not giving a complete picture. But in the SoP, or equivalent, only mention music if it is somehow relevant to your plans in neuroscience.