Recruiter's perspective: One problem I see when candidates list too many categories is that you end up with too large a 'Skills' section on the resume, and then candidates wonder why their resume is 5 pages long. Being thorough is good, but you also want to be sure to keep the resume to an acceptable length. I've seen skills sections broken down into 10 categories, which ends up taking an entire page for some.
I usually have candidates use Languages, Databases, Operating Systems, and then a catch-all such as Tools. You can include frameworks, app servers, testing tools, those API's, and a host of things in the Tools section.
Keep in mind the initial reader/screener is probably someone in HR that is looking for a particular buzzword, and where it is categorized is often beyond the scope of resume screeners. You certainly want to categorize as accurately as possible, but if it's taking up half a page of your resume you should reconsider, especially (as in the example above) if you only have one single item to list under a category.