Edit in 2021: Go to: Preferences | Editor | Code Editing. Find the following section in General: Highlight on Caret Movement. Check the following checkbox: Highlight usages of element at caret.
Bookmark files, packages, folders, and modulesIn the Project tool window ( Alt+1 ), right-click an item that you want to bookmark and select Bookmarks | Add Bookmark ( F11 ) or Add Mnemonic Bookmark ( Ctrl+F11 ).
From the main menu, select Edit | Find | Find in Files Ctrl+Shift+F . In the search field, type your search string. Alternatively, in the editor, highlight the string you want to find and press Ctrl+Shift+F . PhpStorm places the highlighted string into the search field.
Here is a nice feature: Autoscroll to Source and Autoscroll from Source.
It is available in all IntelliJ products .

Should be used if you do not like when your Project View panel gets changed/moves without your consent.
Navigate | Select in... | Project View
Alt+F1, 1 for Windows/Linux
⌥+F1, 1 (or fn+⌥ Opt+F1, 1) for Mac OS
You may also click on "target like" icon on actual Project View panel with your mouse:

If you wish to use shorter/single shortcut instead of standard 2-step shortcut:
As of some 2017.x version (or maybe even 2016.x) the IDE has own dedicated Select in Project View action (so no need for additional plugin). You can find it in Keymap under the Other branch (hint: use search box to narrow the list).
Can be used if you do not mind (or even want) to have Project View panel keep focused on currently edited file (so it scrolls/moves up and down/expands when needed).
NOTE: with frequently switching between the files (e.g. CSS & HTML) when you have a lot of files in your project such "scrolling" may become quite annoying pretty fast (especially if such files are located in the invisible-right-now part of the project tree).
Activate Autoscroll from Source option in Project View panel (right click on tool window header bar/title or use menu under "gear" icon):

In modern versions (2020.3 and newer) that option was renamed and is now called Always Select Opened File:

Just click the circular icon (with tooltip Scroll from Source) to navigate in the project directory tree and highlight the corresponding active file in the PhpStorm editor.

On PhpStorm 2020.3 you have to click the cog icon in the project pane and select Always Select Opened Files:

The above answers are all valid but unfortunately you'll have to enable them for each project.
There's a plugin from Jetbrains that will enable this behaviour by default for all new projects.
http://plugins.jetbrains.com/plugin/7575?pr=
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