I dived into the code of my new favorite IDE Netbeans these last days and came up with an extension module, which adds PHP CodeSniffer Support on a per file basis to make my life much easier. It shows warnings and errors as annotations to the Editor and marks the affected lines in yellow and red.
[STRIKEOUT:My Java skills being very bad, it will only work on Linux currently, since the PHP Code Sniffer "binary" is hardcoded into the Java Source code. You have to create a "/usr/bin/phpcs2" executable, which is a wrapper that looks like:]
With Manuals extensions (see the comments) the module now works without the wrapper script. It might even work under Windows now. Yet now the Zend Coding standard is enforced though. I am working on making that one configurable next.
You can install the NBM module install file from the GitHub repository into Netbeans and it "should" work then.
I hope to get more familiar with Netbeans in the future to add some more PHP tools and enhance Code Sniffer support.