Pomodoros is a great metric. Katja Grace makes the case for that here: http://www.overcomingbias.com/2012/08/on-the-goodness-of-beeminder.html (she just calls them blocks of time).

I think raw number of hours is a fine metric too though. Discretizing into pomodoros has both advantages and disadvantages.

If you can quantify actual output, that might be ideal. Like how we track User-Visible Improvements to Beeminder. You might expect that to be too fuzzy a metric but we found a criterion that's been rock solid for years now: If we're willing to publicly tweet it then it counts. Pride prevents us from ever getting too weaselly about it.