Chrome desktop notifications use notify-osd?
Is there a way to make Chrome/Chromium's notifications use notify-osd instead of the ugly boxes it uses by default?
Yeah: Chromify-OSD.
This can be installed from the Google Chrome Web Store.
To install it, just go to the webstore and click the "Add to Chrome" button - it'll do the rest.
To use it, you'll probably need to restart Chrome, at that point it should be working.
All bugs should be reported to the launchpad.net project page - for more on reporting bugs, take a look at this question: How do I report a bug?
Since NPAPI is gone, pretty much every solution is dead. It looks like there's currently only one solution, and it isn't great.
Libnotify Notifications in Chrome
It is rated very low, but that's most likely because it is still incomplete. It also requires a piece of software to run on the machine itself, so it's not the most easy installation.
However, if you can run scripts and are willing to take security risks, this may work great for you, as long as you don't expect it to work with everything (the author says Gmail is currently in the works).
Sadly, it seems that Google's decision to kill NPAPI in Chromium has also killed this convenience measure.
I will continue to research, but at the moment, this is the only solution I can find that isn't over a year old.