For all projects I have gulpfile.js in the project's root (also bower.json, package.json and node_modules).
In PhpStorm Settings > Languages & Frameworks > Node.js and NPM I can see all the (local and global) packages.
However, in some projects PhpStorm shows the npm and Gulp tool windows... and in other projects it doesn't.
Anybody else ran into this problem? The only (consistent) difference between the projects that have those tool windows and the ones that don't is: the projects for which PhpStorm doesn't show those tool windows are using versioning (either svn or git). I have no idea as why this is happening :|
Solved it...
So, while having the gulpfile.js open, I've right-clicked on the filename tab (works also on the file in the Project tab) and saw that in the right-click menu I have "Show Gulp Tasks". Clicked on that and the Gulp Tool Window appeared... Same for npm (right click menu on package.json). And after that, those 2 tool windows also appeared in the menu: View -> Tool Windows.
It's still weird that on any project I use versioning, they're not already there by default. It must be a bug... But at least this solved my problem.