I am sort of mid-way through transition right now. I have been on HRT for a time, and all the clothes I wear are female, although not overtly feminine.. and I have grown my hair down to about the middle of my back.
So, starting mid-August I have been working for a large, glbt friendly company.. and its going really well! I am happy with the company, and feel generally supported, although I am not out at my work yet. All of my immediate co-workers seem to think I am male, which is great, they have all been really nice. However, in my work I have to interact with many other company employees, who don't know me, and many of them think I am female.
I generally don't try to discourage them from thinking that, as I feel my gender (perceived or otherwise) has no real bearing on my job.
The one time it does matter, however, is when I use the men's restroom, which I use since I am not out yet at work. It seems almost daily that some one is confused by my presence there. I haven't had any terribly negative reactions yet, but I don't want this to become an issue with management. With less than 2 months at this company, I would rather not raise any issues right now.