I don't explicitly indicate my skills and experience with each technology or tool on my resume. Instead, when I provide descriptions of each job and my duties as well as my personal and academic projects, I also mention the core technologies that I've used in support of that position. Every place that I've applied to either asked for a cover letter or provided an application form, which I used to enumerate specific skills that I had (focusing on those relevant to the job description that I was applying to) and described my level of experience with each one.
There are two problems that I see with listing your skills explicitly.
First, you have to tailor your resume even more for each job that you apply to. In order to save space, you are going to want to focus on the skills that are listed in the job description plus anything else that you feel is relevant. You can't possibly list every skill you have - I know that for me, it would take up way too much space. As you gain experience and knowledge, it'll only become harder to choose what to enumerate.
Second, how do you define "expert", "advanced", and "beginner"? Where do you draw the line? Things that I think a beginner should know might be something that you consider to be advanced. Using such ambiguous words doesn't give me any information about you as a candidate for a position. On top of that, languages (or any skill) cover a lot of areas. I could be an expert Java Swing developer, but have no knowledge of Java networking and limited threading knowledge. Am I a beginner, advanced, or expert at Java? Your work experience will let me know what aspects of the language you have used and for how long.
I honestly don't think it's about the skills that you have, but rather what you are capable of learning and contributing to the project, team, and organization. That's the approach I've taken and it appears to have worked quite well for me - I've obtained two six-month co-ops, three summer internships, a TA position, and a full-time job (pending paperwork) with this approach.