The Secret of Mana article that mentioned the picture of the nude woman that the National Scar and Mystic Book enemies sometimes exhibit has been one of the most popular articles on this site. Here are some more blatant examples of videogame characters in the buff.

ActRaiser During the simulation scenes, ActRaiser has you in control of a naked angel. Not much to really speak of, but I used to find it slightly amusing that you can see his little bare ass when he turns around.

Breath of Fire 2 Crawl and 1000 says: Deathevan has chest bursters for penises. FO's Note: I had thought about adding Deathevan to this article before, but his design is so bizarre, I wasn't sure if it really counted.

Final Fantasy Along with the uncanny resemblance Deathevan bears to him, some people on the forums pointed out that the snake thing coming out of the final boss, Chaos, looks like a phallus. I'm not 100% sure of that one. It looks more to me like it's coming out of his abdomen, not his crotch. I'll leave it up for you to decide.

Kid Icarus The final level has topless Venus de Milo statues. Also, the Syren enemy appeared (very) barebreasted in the manual.

The Legend of the Mystical Ninja The Legend of the Mystical Ninja features a Tanuki character with an enlarged and fully-visible scrotum. This was the first image of a "true" Tanuki I had ever seen (not counting "Tanooki Mario"), and I had no idea what I was looking at back then.

The Magic of Scheherazade The boss of Chapter 2, Curly (a mistranslation of Kali) is barechested. This was the first instance of nudity I ever saw in an NES game (although Kid Icarus came earlier, I didn't actually play it until later), and I was a little surprised by it. The demon is clearly referred to as being "female" in the game's dialogue, as shown in this screenshot.

Rise of the Robots While some of these entries make me wonder how they got missed (or allowed) by the censors, this one I could understand, because it's difficult to see on a normal television set, especially against all the game's dark and/or blue backgrounds. However, with the extra clarity emulation grants us on a computer, it's pretty obvious that from certain angles, the Cyborg's junk is clearly visible. It's especially noticeable when he does the kick that causes him to turn his ass towards the screen. To prove that it's not part of the background and I'm not trying to shanghai you here, there it is again on a different background. And the crouching kick view... it's just a single pixel, but it's there. While it's not really noticeable from most front views, it is from this one. All I have to say is, why? Why, why, why, why, why???? Why would they think you'd want to see that while fighting? (Although, why they thought you'd want to play this game at all might be an even better question.)

River City Ransom If you pay a few dollars to use the sauna at Pop's Health Club, you're treated to a nice view of Alex's naked chubby ass, complete with visible moles (or dimples). I'm sure that's just what everyone wanted to see. I remember a time when the internet was young and this scene was the game's main claim to fame.