I do all my exercise and work outs immediately after I eat dinner. I like running and will typically run a mile or two a few days a week. I am trying to increase frequency and mileage while gaining weight. I am pre-diabetic so running immediately after eating helps keep blood sugars under 200. This also helps build muscle as nutrients are available during exercise. If I don't eat a full meal before an exercise I will drink a shake containing whole milk, yogurt, whey protein, eggs, and a banana (for flavor).
Depending on time restraints I will do other workouts (shoulder shrugs, bicep curls, bicycle kicks, push-ups, squats). I try to cycle through different routines to give muscles time to rest and rebuild. High weight and low reps with a concentration on breathing control yields the best benefits for me, both in terms of muscle gain and lung improvement. I'm amazed as how much a simple weight workout will cause me to cough when I'm practicing good breathing control. Since gyms don't really allow for forced coughing routines between exercises I stick to working out at home. My home gym has it's limitations though (right now I use 5 gallon water jugs to do shoulder shrugs haha). I typically do an albuterol and hypertonic saline after a workout. I may start trying albuterol before and saline after though, since I find the sooner the saline hits my lungs after exercise the more I produce.
Personally, I think swimming is probably the very best exercise for CF. When I was living with my parents I used to swim laps after work both on the surface and holding my breath under water while swimming the full length of the pool (typical suburban in-ground pool). There was so much pressure on the lungs, breathing control, and physical exertion involved that it always caused me to cough stuff up. The only drawback is that it burns many more calories than other exercises because of the additional energy needed to heat the body in the water. From what I've read you burn more calories from heat exchange than from the physical exertion of swimming (thus why Michael Phelps eats 12,000 calories/day). So if you really struggle to maintain and gain weight (like me) swimming may not be a great option. Of course heating your pool to bath-like temperatures, or wearing a wet suit could solve this problem haha.