How to change Chrome highlight color
There is now a new and more easy to use chrome extension that does this. Its called Custom Highlight and you can install it here.
There's also this Chrome extension called Highlight Color which does exactly that
And actually looks pretty neat from what I can see from the screenshots.
If you're on a mac, you can change the system highlight color, which will change the color of the highlighting in chrome.
System Preferences > General > Highlight Color