Hourglass - Hourglass is the most advanced simple countdown timer for Windows.
TIMEBOX - An advanced timer for professional meeting facilitators
wnr - Better than pomodoro, this timer app balances work and rest.
Gestimer - For those little reminders during the day
MetaClock.com - MetaClock is an Online Alarm Clock that can play YouTube videos and uploaded MP3s as an alarm tune. It supports Chromecast which means you can turn your TV or stereo system into an alarm clock. No installation is needed, it can also work offline.
Floating Timer - Features both a countdown timer and stopwatch that will float over other apps.