for m e, it depends upon focus.
ok, for instance, my husband's focus is gaining lean muscle mass. so, his focus is weight training. he does his weights first (after a 10 minute cardio workout), and then he does his running after (30-45 minutes depending upon the day, his particular energy levels, the difficulty of his weight training work out that day, etc), and then after that, he does about 15-20 minutes of yoga. Since the focus is lean muscle, he does muscle first, then leanness via cardio, then stretching/yoga to support overall balance, flexibility, and health.
in my case, i focus on yoga. so, any cardio or weights that i do, i do for the purpose of fun/look/leanness. i spread mine out throughout the day, because i can. The only thing that i go 'full out' on is yoga--the rest is about 80%.
so, for me it works like this: 30 minutes moderate cardio--30 minutes yoga. later on, more yoga, and then later on, maybe more cardio, but then definately yoga after. on weights days, i do weights (30 minutes), cardio (30 minutes), and then supportive yoga (to stretch out and balance)--about 15-30 minutes. then, latter in the day i'll do more yoga to work on yoga.
so, it really depends upon what you want. If you want to emphasize lean-ness,c ardio vascular health, etc, then focus on cardio. If you want to emphasize muscle development and strength, then focus on weights. If you want to focus on flexibility and and muscle balance (and cardio too, actually), then focus on yoga.
up to you--whatever you want!