Google Chrome opens in a new window in a new launcher icon

rm $HOME/.local/share/applications/google-chrome-*.desktop

From then on, Unity launcher won't create a second icon when you open Chrome.

I suspect that file is created when Chrome navigates directly to a site upon launch. The google-chrome-*.desktop file gives Unity a different Name value for Google Chrome than that defined when the application was added to the launcher, so Unity launcher doesn't know it's the same application.

This fix helped me out when the problem came back after each update.

edit /usr/share/applications/google-chrome.desktop

There are three entries in this file:
[Desktop Entry], [NewWindow Shortcut Group] and [NewIncognito Shortcut Group]

After each entry add this line:

StartupWMClass=Google-chrome-stable

Found this solution here:
http://kb.openstudioproject.com/content/fix-double-google-chrome-icon-docky-and-plank

And a bug report about it here:
https://code.google.com/p/chromium/issues/detail?id=378881#c13