Python timer app with a GUI for time input and display of time remaining. When timer expires, it jiggles the icon in the unity launcher until the GUI window receives a focus-in event.

my-timer-2.desktop

[Desktop Entry]
Name=My Timer
Exec=/home/markham/scripts/timer.py
Icon=/usr/share/icons/cute.jpg
Type=Application
Terminal=false
StartupNotify=true
Categories=GTK;GNOME;Utility;

my-timer-2.py

#!/usr/bin/python

DESKTOP_FILE_NAME 	= 'my-timer.desktop' # you need to create this file
INITIAL_TEXT		= '0:0:1'

from gi.repository import Unity, GObject, Gtk
import re, StringIO

class TimerWindow(Gtk.Window):
	def __init__(self):
		Gtk.Window.__init__(self, title="My Timer")
		self.connect("delete-event", Gtk.main_quit)
		box = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL, spacing=6)
		self.add(box)
		self.entry = Gtk.Entry()
		self.entry.set_text(INITIAL_TEXT)
		self.entry.connect("activate", self.activate_entry)
		# self.focus_btn = Gtk.Button()
		# self.focus_btn.set_label(u"\u2766")
		box.add(self.entry)
		# box.add(self.focus_btn)
		self.show_all()
		self.finished = False

	def reset(self, a, b):
		self.disconnect(self.focus_in_handler)
		self.finished = False
		print 'reset'

	def activate_entry(self, entry):
		self.start_time = GObject.get_current_time()
		text = entry.get_text() 
		print text
		arr = re.split('\D+', text)
		n = len(arr)
		hr = int(arr[-3]) if n >= 3 else 0
		mn = int(arr[-2] or 0) if n >= 2 else int(arr[0])
		sc = int(arr[-1]) if n >= 2 else 0
		self.total_seconds = sc + 60*mn + 360*hr
		print 'Timer for', self.total_seconds, 'seconds'
		launcher.set_property('progress_visible', True)
		self.set_focus(None)
		self.update_progress()
		GObject.timeout_add_seconds(1, self.update_progress)

	def update_progress(self):
		delta = GObject.get_current_time() - self.start_time
		progress = delta / self.total_seconds
		if progress >= 1:
			if not self.finished:
				self.finished = True
				launcher.set_property('progress_visible', False)
				self.entry.set_text("TIME'S UP!")
				GObject.timeout_add(200, self.jiggle_unity)
				message = Gtk.MessageDialog(None, Gtk.DialogFlags.MODAL, Gtk.MessageType.INFO, Gtk.ButtonsType.OK, "TIME'S UP!")
				message.set_keep_above(True)				
				btn = message.get_child().get_children()[1].get_children()[0]
				btn.connect('activate', lambda x: message.close())
				btn.connect('clicked', lambda x: message.close())
				message.run() # Blocks. Should return -4; Before calling this, I could add self.set_focus(message), but I don't want to accidentally hit Enter at the wrong moment and miss seeing the modal dialog
				self.focus_in_handler = self.connect("focus-in-event", self.reset)
				message.close()
				self.set_focus(self.entry)
			return False
		else:
			launcher.set_property('progress', progress)
			if not self.entry.has_focus():
				remaining = self.total_seconds - delta
				mn = remaining / 60
				hr = mn / 60
				stamp = StringIO.StringIO()
				stamp.write('%d:%02d:%02d' % (hr, mn%60, remaining%60))
				self.entry.set_text(stamp.getvalue())
			return True

	def jiggle_unity(self):
		if self.finished:
			urgent = launcher.get_property('urgent')
			launcher.set_property('urgent', not urgent)
			return True
		else:
			return False

launcher = Unity.LauncherEntry.get_for_desktop_id(DESKTOP_FILE_NAME)
win = TimerWindow()
Gtk.main()

It would be nice if you can integrate with messaging menu integration as well.