I recently started using freckle (letsfreckle.com). The timer is great, as is the freeform project creation and logging.
just keep a small pad of paper in your back pocket. the longer you spend searching for faster/fancier/more efficient/cooler ways to track things, the more time you're simply wasting.
Just start doing it and write down your progress.
I use pomodoro.app on my Mac, the timer function on my iPhone, and may download a dedicated iPhone app at somepoint.
I personally don't currently use the history feature of pomodoro (what previous tasks were, how many were completed, etc.). Just defining a task, focusing for 25 minutes, and tracking break time are the things most important to me.
I'd ideally like to have many pomodoro "time jars", which track how many pomodoros I complete for a particular larger goal over some time period. When the time jar is full, for some personal definition of full, you've completed the goal. Haven't found a good app for this, so pointers would be appreciated. Might hack up something simple for the iPhone this summer...
To the commenter about time optimization wasting time, if that's all you do instead of Actually Working, sure. But to never profile your work flow, and never experiment with new methods... not only is that boring, it's inefficient over the long term. My personal productivity philosophy definitely includes a meta step for reflection and experimentation http://cosmicrays.wordpress.com/2009/12/20/productivity/