What's an example where of a feature of cc or ld that you can't detect with feature detection?

Shell scripts are turing complete and can do arbitrary I/O. In theory you can write a feature detection for any feature by compiling, linking, and running a test program. If the feature couldn't be detected this way, then it would be useless.

Likewise, JavaScript and DOM features should always be detectable by eval(). I guess one instance where it's impossible is if the API changes the pixels on the screen and does nothing else.

Although you can actually detect this in some cases with JavaScript! JavaScript can leak information through the colors of attributes on the screen, e.g. you can tell if a user visited a site by looking if the link is purple!