Besides pay, men are normally granted more novelty things around the workplace then women. I have experienced that men are normally not punished for coming into work a little later and are granted extra privileges such as an extra day off, longer vacation days, and more paid sick and personal days. Again, this isn't the case everywhere, but I can only talk from my own personal views and experiences. Another privilege that I experience due to my gender is in the view of safety. Being male, I have realized that often I am not worried about my safety in regards to other people hurting me. Women are raised to always be cautious of being attacked and in turn this makes them believe that they are weaker. Women are often not seen walking alone late at night or leaving their guard down in the company of strangers. Yet, men don't have this worry to the same extent. Men don't think anything of walking through a dark parking lot late at night, or walking past a group of people on the street. Although I"m not sure if this could be viewed as a privilege, I feel that I do indeed benefit for this since it is a societal norm to raise women in one mind set of safety and men in others. That's why families with a son and daughter often set different rules for the two children. The son is allowed to go to a party at age 15 and not have to give any information of his whereabouts as long as he is in by curfew, but the daughter has to be with friends, the parents want to know where the party is at, if the parents are home at the house of the party, and normally she has an earlier curfew.
I also think that in general, there are ways in which men deny their privileged position. Back to the example about safety, men know that women are more susceptible to being attacked or raped when walking alone at night, yet they will not say that it is because they are female. Men will often say that they could have just as easily been the ones to get attacked or mugged.