You can add each of these scripts to Pomodoro.app's start/end AppleScript actions and disable / enable notification center as well as quit / launch some apps.

disable_notificaiton_center.applescript

tell application "System Events"
	tell process "Notification Center"
		key down option
		click menu bar item 1 of menu bar 1
		key up option
	end tell
end tell

--quit some apps that I tend to check too often when I should be focusing on coding.
try
	set quitApps to {¬
		"Tweetbot", ¬
		"Sparrow"}
	
	set num_of_apps to count quitApps
	
	repeat with i from 1 to num_of_apps
		set varapp to (item i of quitApps)
		tell application varapp to quit
	end repeat
on error
	tell the current application to display dialog "An error has occurred!" & return & "This script will now quit" buttons {"Quit"} default button 1 with icon 0
end try

enable_notification_center.applescript

tell application "System Events"
	tell process "Notification Center"
		key down option
		click menu bar item 1 of menu bar 1
		key up option
	end tell
end tell

--re-enable the previously quit apps when you come up for air
set launchApps to {¬
	"Sparrow", ¬
	"Tweetbot"}

set num_of_apps to count launchApps

repeat with i from 1 to num_of_apps
	set varapp to (item i of launchApps)
	tell application varapp to activate
end repeat