Chrome's notification boxes have three major complaints from me:
A. They don't automatically close. (I think you can change this for each web app individually, but I would like a browser-wise setting). This wouldn't be a big issue, if not for...
B. The close button is freaking tiny. I can dismiss Growl notifications by clicking anywhere on them, which is much nicer on a laptop than trying to move to a small button.
C. The notifcation windows resemble what Apple calls panels. [1] The problem is, "Panels float above other windows and provide tools or controls that users can work with while documents are open." [2] The user isn't meant to be closing panels often, which is why the title bar can be small. Chrome's notifications feel out of place in that regard.