At a glance, the only suggestion I disagree with is PHPjs (http://phpjs.org/).

Many of its functions are badly implemented.

Examples:

http://phpjs.org/functions/array_fill:314 (doesn't even return an Array type)

http://phpjs.org/functions/array_unshift:347 (using `arguments[n]` instead of the arg name)

http://phpjs.org/functions/call_user_func:363 (unnecessary and broken usage of eval)

Also: it's essentially porting a bad API to a language where much of it isn't needed. (e.g. array_push).

It's best to avoid PHPjs if you're looking to learn JS IMHO.