The flexibility training you do depends entirely on what else you want to achieve. You could try Ashtanga, Hatha, or even Kundalini. Each style comes with it's different benefits. Ashtanga is focused on strength building, it's a very long and intense workout; Hatha is a lot more focused on restoration, and is my favourite; Kundalini is a great way of working with breathing techniques and meditation, although it can be a bit too spiritually inclined for some.
I practice 90 minutes of Ashtanga in the morning, and some restorative yoga after Jiu Jitsu. The best thing to do, in my opinion, is find what works for your body and develop your own "style". Do not force yourself to stretch to where you think you should be, you should never experience pain when you stretch.
I'm enjoying following David Procyshyn's Hatha Yoga videos, but watch the forward bends if you aren't already flexible. The start of this video is part of my warm up before Jiu Jitsu, as it's great to loosen the hips. I use my old blue belt for the postures that require a strap.
http://www.youtube.com/watch?v=gDQNqZMv1V0
The best thing to do is find a reputable Yoga school near you and regularly attend class there. Your technique is extremely important if you want to avoid silly injuries when you practice alone. Without an experienced teacher to adjust your early mistakes, you could develop bad habits, causing more damage in the long run, rather than strengthening the body.