A bit torn. While I love Dirge of Cerberus, and purple, purple and yellow are a very harsh combination (they're opposites, after all), so it's hard for me to get her Dirge of Cerberus outfit high.
Her original one is nice, the color scheme is good, the whole design is nice, but essentially just that. Personally, there's nothing else that calls my attention.
Her Advent Children one is a really cool one too, again Square scoring only in outfits in that film, but I can barely see every detail of it, making it hard for me to appreciate it to the fullest (and although I have watched the film, Yuffie doesn't appear that much, so her outfit didn't stay printed in my mind).
Her Crisis Core and Before Crisis, which are a little similar (just a color change, essentially), are really cool too. I prefer blues over yellows, so I'll take Crisis Core more than Before Crisis.
And of course, we can't forget. Her awesome cape. That's definitely my favorite thing of any outfit. The cape she uses in both InterMission and Dirge of Cerberus is awesome, even if it is moogle-themed. I think it's the fact that it's a little shredded and not your perfectly-just-finished-made-unscathed cape that makes me love it.