Google Apps' browser-based calendar notifications are great, but annoying when they appear on top of the email you are in the middle of composing. Here is a way to disable these notifications in favor of an alternate "Gentle Notifications" option that blinks the alert to you without shifting the focus of your work.
Here's the Google page describing it. Note that you'll first need to enable Google Labs, the experimental feature set in Google Apps; those steps are at the top of the article. Then expand the section further down titled "Gentle Notifications" for this specific feature.