I don't formally use Pomodoro, but I have adopted the use of the 25 minute timer for health reasons. It's well known that sitting for extended periods is not good for you, but I don't want to switch to a standing desk--standing for long periods is also bad for you.

Best is to use a sitting desk, but to get up every so often and move around:

   Sit to do computer work. Sit using a height-adjustable,
   downward titling keyboard tray for the best work posture,
   then every 20 minutes stand for 2 minutes AND MOVE. The
   absolute time isn’t critical but about every 20-30 minutes
   take a posture break and move for a couple of minutes.
   Simply standing is insufficient. Movement is important
   to get blood circulation through the muscles. And movement
   is FREE! Research shows that you don’t need to do vigorous
   exercise (e.g. jumping jacks) to get the benefits, just
   walking around is sufficient. So build in a pattern of
   creating greater movement variety in the workplace (e.g.
   walk to a printer, water fountain, stand for a meeting,
   take the stairs, walk around the floor, park a bit further
   away from the building each day).

Source: http://ergo.human.cornell.edu/CUESitStand.html

Note how they recommend getting up every 20 to 30 minutes--a perfect fit for a Pomodoro timer.

I find that the timer doesn't interrupt being in the zone--I can just keep thinking about what I'm working on while I walk around for a couple minutes, and the fitness break is essentially no interruption at all. If I'm not in the zone, then after the break I will do a Pomodoro-like thing and check email and reevaluate what I should be doing before getting back to work.