If all the talk about sets and reps from my last post sent shivers up your spine then there is a simple solution for building strong muscles and an agile, flexible body: bodyweight exercises. Bodyweight squats, push ups, pull ups, and crunches/situps come in all shapes and sizes and can really get the heart pumping and make you lean and strong. Plus, they increase flexibility and especially target the lower back.
Bodyweight exercises and calesthenics are standard practice for martial artists, boxers, rowers, and gynasts. You won't get big but you'll get strong and agile. Here is a simple set of bodyweight exercises to do as a warmup or as a strength training workout. Aim for high reps total on these -- 100 or so -- and build up slowly to that number if you've never done the exercises before.
Squats (hindu squats are a favorite)
push ups (dive bomber style work the shoulders great)
sit ups (pilates-style curl ups)
back bridge
Another alternative is to do a 20-40 minute "power yoga" routine. Baron Baptiste has some excellent DVDs, books and tapes. Steve Ross can be found every morning at 6am on the Oxygen channel. Power yoga emphasizes bodyweight movements that will build strength and endurance. You don't have to get into the metaphysical aspects of it -- that's probably what you have running for :)