CrossFit is getting hugely popular in pilot circles...
I run. Run outside if I can, otherwise its indoors on a treadmill. Crappy hotel treadmill? Then I get on an elliptical or, worst case scenario, stationary bike. For me, cardio is king and I use being on the road as an opportunity to see new cities and train for the road races that I run.
As far as food goes...when I was at a regional I packed a small cooler. I took 4 peanut butter sandwiches, almonds, Power or Cliff Bars, fruit cups, microwavable low-sodium soup, bananas, etc. This could sustain me for at least 2 days and not only helped save per-diem but kept me away from crappy airport food. My most common airport snack was chocolate milk. Yes, that's right, I looked like I was 6 years old...but even with HFCS for the flavor it was still substantially healthier than 90% of the other choices available.
Now that I'm corporate and have a credit card for expenses, I can buy pretty much whatever I want/need to for meals. I try to control portion size, get more vegetables than potatoes, limit myself to one beer (if any) and no more than one soda per day. I also single-handedly keep a couple Smoothie King franchises in business.
Unlike others, I'm a coffee junkie. Typically I have two cups (maybe 16oz) with milk for breakfast and sometimes that's all I have - it typically sustains me to lunch with minimal hunger pangs.
The lifestyle associated with this profession requires dedication & discipline to maintain a healthy body...but for me all it takes is one stroll in a major airport or FBO to see all the morbidly obese pilots with their guts protruding from the bottom of their shirts to motivate me to go out for a 4 miler!