I do both, and for the most part I prefer yoga. It really all depends on my body's needs on a given day, though -- I have chronic sciatica on my left side and usually yoga does wonders for it, but sometimes Pilates or a combination seems to do a lot better. Yoga is great to stretch it, but I find that I really have to do it daily or the pain comes back. With yoga -- completely pain-free, and I tend to be much more alert throughout the day than when I don't exercise.
As for men doing yoga -- no, it's not un-manly! In fact, I do attend yoga classes twice a week, and there are a number of male athletes, and a number of 40+ men who attend regularly. The athletes all say that they have not been injured since they started yoga, and one is recovering from a knee injury. Most of the older men are there either to stay nimble as they age, or because their doctors suggested it as an alternative to drugs for chronic pain. One of my favorite instructors is also male, and historically there has been no gender bias -- I'm really not sure why it's perceived as more feminine now.