This is a word count tool used in localisation projects, because it supports a variety of formats, including most common tagged and scripting languages. It costs £320 but a 15-day demo is available for isolated needs. It says it works with PHP but it did not work when we tried to do word counts for sites using PHP.
This is another word count tool that also supports most common formats but the results were not good either, as it included duplicate files (it doesn't recognize them as duplicate files because their file paths are different). The standard version costs £36. There is a business version with additional features like file converting and counting of files in other computers for £62.