Considering you can see Boss's and Kaz's...bulges....in the beach "episode", I consder alot of the examples of naked dudes with each other in MGS is for homoerotic in nature, which is ultimately fanservice to a crowd.Raiden's situation is meant to make him feel vulnerable more than anything but I can see the sex appeal angle as well to a certain extent. Not to dismiss that a naked man can't be fanservice, but I believe Kojima wanted it to be more comedic and ridiculous, similar to Johnny in MGS1.
Volgin torturing Naked Snake (who pisses his pants in fear), while clearly horrible, has alot of sexual undertones (consdering Volgin is noted to be bisexual)
There's also Ocelot torturing Snake in MGS1, which taken with the later revelations of Ocelot being gay/in love with Big Boss, makes it seem like a really twisted fantasy to him. Again sexual.
There's alot of creepy fanservice in MGS no doubt, but it dosen't just happen to the woman. It's with the guys too, alot of the time.