i love running. i'm pretty athletic, but it i had to choose one form of exercise that does the most for me physically, it'd be running. the best shape i've ever been in--and i mean this regarding my muscles, my heart, my joints (as in flexibility and suppleness), and overall general well-being--was due to running. i used to run 5 miles in 45 mins (uphill and down) every other day, alternating with some form of aerobics on 'off' days. when i got pregnant, i quit running and started hiking. anyway, i'm still working back up to 5 miles now.
cross training is where it's at, i think. now i prefer to strenuously hike one day, run the next, and mountain bike the next. followed by a day 'off.' mountain biking really builds quad muscles more than running, but running makes me have better breath control. hiking is just a good break for my mind, but it's still great exercise.
i know runner's world website has a training program cuz my marathon runner friend uses it and likes it. but i always just listen to my body, and increase my distance first, and speed after. if my knees hurt, i know it's because i'm trying to go too far too soon. i just wear New Balance shoes, and have never had a problem with my feet, but i have a decent arch.