The most important thing to first do is make a list of which attributes you would like to improve. For example, if you're looking to improve absolute strength, weightlifting would be more effective than running. However, if increased aerobic capacity was your goal, the reverse would be true.
For me, I'm looking to improve muscular endurance more than anything else, so I use higher rep weight training, along with bodyweight exercises for variety. If I was focused more on absolute strength, I'd ratchet up the weights and bring the reps down. I also hit the heavy bag quite a bit, as I feel it's very efficient -- it allows me to work technique and endurance simultaneously. That's where I devote most of my training effort. Personally. I hate running, because I stink at it and it hurts my knees. So for aerobic training (which is necessary for general health as well as MA training) I ride the bike and do my forms back-to-back (efficiency again). I try to stretch as much as possible, but I really don't do as much as I should.
So for me, "the list" would look like this:
Attribute Activity
----------- ---------
Muscular Endurance Weight Training, Bag Work
Cardiovascular Endurance Cycling, Kata
Flexibility Stretching
That would all be apart from technique practice and drills. A lot of these activities will also overlap attributes, but that can be a good thing too.