I might not be the best person to ask, but I do have a lot of suggestions.
As for me, personally, I started running when i was in 9th grade for Cross Country/track. That stopped after winter 9th grade, because the coach was an arse, but it got me into shape rediculously fast. So I would definitely recommend running. Vary it between distance (for endurance) and sprinting (for the speed/short term bursts).
I also did taekwondo for a very long time (still am) so that kept me in shape after I quit CC/Track.
But, as far as a workout regiment for getting into/staying in shape, specifically tailored for what you'll need for parkour (which is.. haha.. everything. >.>):
*Running. Mentioned earlier, vary the workout. Do both distance runs and sprints, do hills and do flats. This builds stamina, speed, endurance. It's also the best way to lose weight. I find it best if you find a friend to run with.
*Pullups. Overhand, underhand, one hand, no hands, however you can do them. Don't set a limit. Don't say "3 reps of 10." Do as many as you can until you fall off the damn bar. These will help you with getting over obstacles.
*Crunches. Everyway you can do them. Do sets of standard crunches, and then try doing sets of touching your left elbow to your right knee, then vice versa. Upside down crunches are fun, if you can do them safely and comfortably. This is very important in strengthening your "core" (torso area, basically.) which is important in a lot of parkour techniques.
*Push ups. Strengthens arms, important for some vaults, pulling yourself over obstacles, etc.
Those are a few pretty standard exercises, but you don't really need anything exotic. Strength helps in a lot of parkour, but you don't need to be ripped or anything. (Although it doesn't hurt.. >.>)
I'm not a big fan of gyms. I went to a gym once to work out.. it was lame. If you use these exercises to get into shape/stay in shape, just practicing parkour will help build the muscles you really need.
When you're in a gym, you're working with weights and machines. When you're actually outside, pulling your body over a wall ontop of a building, you're actually using those muscles for what you're planning on using them for. You're also not just using your biceps. You're using your entire body to get over that wall, because if you fall, you die. (Simulated death. :p) So it's not like lifting weights and being buff, you're using your entire body to overcome an obstacle, which is another important part of parkour.
Flow and synergy of the body is very important. If your muscles can't work together optimally, how do you expect to use your body to the best of its capability?
Anyway, that was a bit longer than I had planned... :p
Final statements: If you're in shape, start practicing small things. Rolls, lazy vaults, things like that. Condition yourself with small drops, i.e. jumping off picnic tables, perfecting your roll from there. Then go a bit higher, perfect roll from there, etc. Do NOT start by jumping off a building. This is stupid, reckless, and dangerous, and it gives parkour a bad name and you will probably die.
If you're not in shape: Focus on the exercises I listed above for about a month, or until you see dramatic improvements in you abilities. I would focus on running out of all of them, but don't neglect the situps, pushups, and pull ups.
Any further questions? You can post, or IM me if you want to talk one on one. I love to talk parkour... (as you can tell.)
[edit- Zell- because teenagers are stupid <string of explitives deleted>.]