I have looked at all WHATWG tests.

Sorry for the delayed review, I missed the notification of the first ping and was traveling for the second one.

I'm still having some troubles with the “include fragment” vs “exclude fragment” tests, since it's hard for me to match up which “include” test belongs to which “exclude” tests (or to verify if they actually come in pairs).

I would suggest refactoring the fragment tests to always include both the include and the exclude parameter, so basically 4 “assertions”:

var_dump($uri1->equals($uri2, Uri\UriComparisonMode::ExcludeFragment));
var_dump($uri2->equals($uri1, Uri\UriComparisonMode::ExcludeFragment));
var_dump($uri1->equals($uri2, Uri\UriComparisonMode::IncludeFragment));
var_dump($uri2->equals($uri1, Uri\UriComparisonMode::IncludeFragment));

This allows one to immediately see if the fragment inclusion changes something or not.

If these two comments are fixed this LGTM. Thank you and sorry for taking this long to review.