Some martial arts practitioners have a bad habit of using the movements of their art as conditioning. To get "in shape" they'll practice basic movements, either by themselves or in free sparring, deep into exhaustion. I understand the impulse - it seems like killing two birds with one stone. You get in lots of reps of your basics and develop your endurance all in one fell swoop. There are a couple of basic reasons why it isn't, however, a good idea:
First is the safety issue. Sparring yourself into exhaustion is probably a good idea if done very sparingly. Do it often, however, and you're asking for an injury. Think about it - what happens to your control and reactions when you're exhausted? You lose both. During free sparring that's asking to get hurt. Do it three times a week and what do you think will happen?
Second, and a bigger issue, is the neurological development question. Your nervous system respond to repetition. The more you do something the more those nerve activation patterns get sort of burned into your system, the more automatic that skill becomes. And your nervous system remembers best the last thing you did in a practice session. So what happens when you throw 200 kicks, and the last 50 are sloppy and slow because by the time you did them you were exhausted? Your nerves remember those 50 sloppy, slow kicks. If your partner does 100 sharp, snappy kicks, then runs sprints or whatever to finish the workout, he could be improving his kicks more than you despite doing half as many reps, because his nervous system will remember the sharp, snappy repetitions.
I'm not saying to quit your workout while you're still fresh. I am saying you should quit your practice of martial arts techniques while still fresh. To improve your conditioning you should end practice with some exercises that are not part of your art that will force you to dig deep into your oxygen reserves. We can call these exercises finishers. They're in your workout at the finish of the workout, and they're put in place to finish you!
There are lots of possibilities for finishers. Running some sprints would work. This would be a bad idea for a sprinter, of course, for the same neurological reasons I mentioned earlier, but as a martial artist you're not worried about maximizing your time in the 100m run. Shadow boxing? Not so good - remember, you'll get sloppy as you get tired, and your brain will remember your sloppy techniques.
Finishers should be low skill, safe, and involve as much of your body mass as possible. Wrist curls are an obviously bad idea - working your forearms in isolation just isn't going to make big enough inroads into your body's oxygen carrying capacity. The same goes for pushups or crunches. You want something where you fail because your heart and lungs are operating at capacity, not because you have a pain buildup in some isolated part of your body.
I like a few exercises. I do power snatches with a light to medium weight - it has to be a weight that you are capable of reverse curling and pressing - no near maximal loads. You don't want to snatch heavy when you're exhausted, because then when your form breaks down you'll end up dumping a bar on your head. Air squats (squats done with no load, at a very quick tempo) are good. Jogging in place could work. Kettlebell swings and thrusters are another nice, rigorous finisher.
Lately I've been doing burpees as my finishers. Squat down, place your hands outside your feet, jump back into a pushup position, do a pushup, hop your feet back up, jump as high as you can. Land. Repeat. I'll do sets of 10, 8, 6, etc. at the end of my workout, when I'm already in oxygen debt from doing kata. The burpees really get my heart and lungs going, and if at the end I'm a little sloppy, that's okay - I'm not worried about developing the perfect burpee. I'd much prefer learning a sloppy burpee to learning a sloppy Seienchin kata.
Post other favorite finishers to comments!