Navy conditioning PDF link: http://www.cnet.navy.mil/nascweb/ocs/conpro.pdf
The Navy stuff is good for checking progress, but it looks really boring. If I'm running 3 miles at the track, after every lap I'll stop (no resting) and go right into 25 pushups. Then start running again without any rest. You can vary the push-ups with sit-ups or pull-ups. This gets you a total workout and makes it less boring.
Also, I found that being on some sort of team or league helps motivate you to get back in shape. When I started playing soccer again I had to get my fat ass in shape because I was getting run over.
Variety is also key (I get bored easily). Schedule your workouts ahead of time so you alternate days between running, swimming, lifting weights, etc... That way you won't get as bored with it and it's easier on your joints that just running every single day. I do something like this:
Mon- run/lift
Tues- soccer
Wed- rest
Thurs- swim/lift
Fri- run/lift